From 113352a8b45175439500895da1c4a9b1bbfa5852 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 25 Jan 2019 11:24:22 +0100 Subject: [PATCH 001/471] [FEATURE] simple sequence tagger --- src/openms/include/OpenMS/CHEMISTRY/Tagger.h | 75 +++++++++++++ .../include/OpenMS/CHEMISTRY/sources.cmake | 1 + src/openms/source/CHEMISTRY/Tagger.cpp | 102 ++++++++++++++++++ src/openms/source/CHEMISTRY/sources.cmake | 1 + 4 files changed, 179 insertions(+) create mode 100644 src/openms/include/OpenMS/CHEMISTRY/Tagger.h create mode 100644 src/openms/source/CHEMISTRY/Tagger.cpp diff --git a/src/openms/include/OpenMS/CHEMISTRY/Tagger.h b/src/openms/include/OpenMS/CHEMISTRY/Tagger.h new file mode 100644 index 00000000000..945c9351de8 --- /dev/null +++ b/src/openms/include/OpenMS/CHEMISTRY/Tagger.h @@ -0,0 +1,75 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2018. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#pragma once + +#include +#include + +#include +#include +#include +#include + +namespace OpenMS +{ + /** + * @brief Calculate sequence tags from m/z values + * + * Current restrictions and potential extensions: + * - all peaks are considered charge 1 + * - first prefix/suffix ion don't give rise to first character in tags (as currently ion types are not specified) + * - modifications are not supported + * - gaps are not supported + **/ + class OPENMS_DLLAPI Tagger + { + public: + // initalize tagger with minimum/maximum tag length and +- tolerance ppm + Tagger(size_t min_tag_length, float ppm, size_t max_tag_length = 65535); + + // generate tags from mass vector @mzs using the standard residues in ResidueDB + void getTag(const std::vector& mzs, std::set& tags) const; + private: + float min_gap_; // will be set to smallest residue mass in ResidueDB + float max_gap_; // will be set to highest residue mass in ResidueDB + float ppm_; // < tolerance + size_t min_tag_length_; // < minimum tag length + size_t max_tag_length_; // < maximum tag length + std::map mass2aa; + char getAAByMass_(float m) const; + void getTag_(std::string & tag, const std::vector& mzs, size_t i, size_t j, std::set& tags) const; + }; +} + diff --git a/src/openms/include/OpenMS/CHEMISTRY/sources.cmake b/src/openms/include/OpenMS/CHEMISTRY/sources.cmake index 63b0ab31144..4805716c202 100644 --- a/src/openms/include/OpenMS/CHEMISTRY/sources.cmake +++ b/src/openms/include/OpenMS/CHEMISTRY/sources.cmake @@ -31,6 +31,7 @@ TheoreticalSpectrumGeneratorXLMS.h SvmTheoreticalSpectrumGenerator.h SvmTheoreticalSpectrumGeneratorSet.h SvmTheoreticalSpectrumGeneratorTrainer.h +Tagger.h WeightWrapper.h ) diff --git a/src/openms/source/CHEMISTRY/Tagger.cpp b/src/openms/source/CHEMISTRY/Tagger.cpp new file mode 100644 index 00000000000..8ba8baaeb80 --- /dev/null +++ b/src/openms/source/CHEMISTRY/Tagger.cpp @@ -0,0 +1,102 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2018. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#include +#include +#include + +namespace OpenMS +{ + char Tagger::getAAByMass_(float m) const + { + // fast check for border cases + if (m < min_gap_ || m > max_gap_) return ' '; + + auto left = mass2aa.lower_bound(m - m * ppm_ * 1e-6); + auto right = mass2aa.lower_bound(m + m * ppm_ * 1e-6); + if (left == right) return ' '; // not found in tolerance window + return left->second; // select first match + } + + void Tagger::getTag_(std::string & tag, const std::vector& mzs, size_t i, size_t j, std::set& tags) const + { + const size_t N = mzs.size(); + // recurse for all peaks in distance < max_gap + while (j < N) + { + const float gap = mzs[j] - mzs[i]; + //cout << i << "\t" << j << "\t" << mzs[i] << "\t" << mzs[j] << "\t" << gap << endl; + if (gap > max_gap_) { return; } // already too far away - continue with next parent + if (tag.size() == max_tag_length_) { return; } // maximum tag size reached? - continue with next parent + const char aa = getAAByMass_(gap); + if (aa == ' ') { ++j; continue; } // can't extend tag + tag += aa; + getTag_(tag, mzs, j, j + 1, tags); + if (tag.size() < min_tag_length_) { tag.resize(tag.size() - 1); ++j; continue; } + tags.insert(tag); + tag.resize(tag.size() - 1); // remove last char + ++j; + } + } + + Tagger::Tagger(size_t min_tag_length, float ppm, size_t max_tag_length) + { + ppm_ = ppm; + min_tag_length_ = min_tag_length; + max_tag_length_ = max_tag_length; + const std::set aas = ResidueDB::getInstance()->getResidues(); + for (auto r : aas) + { + const char letter = r->getOneLetterCode()[0]; + const float mass = r->getMonoWeight(Residue::Internal); + mass2aa[mass] = letter; + //cout << "Mass: " << mass << "\t" << letter << endl; + } + min_gap_ = mass2aa.begin()->first - mass2aa.begin()->first * ppm * 1e-6; + max_gap_ = mass2aa.rbegin()->first + mass2aa.rbegin()->first * ppm * 1e-6; + } + + void Tagger::getTag(const std::vector& mzs, std::set& tags) const + { + // start peak + std::string tag; + tag.reserve(30); + for (size_t i = 0; i < mzs.size() - min_tag_length_; ++i) + { + getTag_(tag, mzs, i, i + 1, tags); + tag.clear(); + } + } +} + diff --git a/src/openms/source/CHEMISTRY/sources.cmake b/src/openms/source/CHEMISTRY/sources.cmake index b9e59ee0e3d..965aca2ca87 100644 --- a/src/openms/source/CHEMISTRY/sources.cmake +++ b/src/openms/source/CHEMISTRY/sources.cmake @@ -30,6 +30,7 @@ TheoreticalSpectrumGeneratorXLMS.cpp SvmTheoreticalSpectrumGenerator.cpp SvmTheoreticalSpectrumGeneratorTrainer.cpp SvmTheoreticalSpectrumGeneratorSet.cpp +Tagger.cpp WeightWrapper.cpp ) From 0036b966436a16b920850f88464d1a51cb1bff65 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 4 Feb 2019 18:30:17 +0100 Subject: [PATCH 002/471] [FEATURE] Aleks: assume charge 1 for fragments with unknown charge (more conservative matching) --- contrib | 2 +- src/utils/RNPxlSearch.cpp | 84 +++++++++++++++++++++------------------ 2 files changed, 46 insertions(+), 40 deletions(-) diff --git a/contrib b/contrib index 06e887232ed..320353cbcfe 160000 --- a/contrib +++ b/contrib @@ -1 +1 @@ -Subproject commit 06e887232ed87631585027e1991ebaef098f7b06 +Subproject commit 320353cbcfe5a85bd36b11f77cb0a7da1b0ac952 diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 98e3b795dcf..6c02e07afb9 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -314,9 +314,10 @@ class RNPxlSearch : // @brief Calculate all chemically feasible fragment adducts for all possible precursor adducts // Same as getFeasibleFragmentAdducts but calculated from all precursor adducts - static PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts(const RNPxlModificationMassesResult& precursor_adducts, - const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, - const set& can_xl); + static PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts( + const RNPxlModificationMassesResult& precursor_adducts, + const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, + const set& can_xl); }; @@ -422,63 +423,68 @@ class RNPxlSearch : #endif for (SignedSize exp_index = 0; exp_index < (SignedSize)exp.size(); ++exp_index) { + MSSpectrum & spec = exp[exp_index]; // sort by mz - exp[exp_index].sortByPosition(); + spec.sortByPosition(); // deisotope - Deisotoper::deisotopeAndSingleCharge(exp[exp_index], + Deisotoper::deisotopeAndSingleCharge(spec, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, 1, 3, false, 2, 10, single_charge_spectra, annotate_charge); + + // set Unknown charge to z=1. Otherwise we get a lot of spurious matches + // to highly charged fragments in the low m/z region + DataArrays::IntegerDataArray& ia = spec.getIntegerDataArrays()[0]; // charge array + for (int & z : ia) { if (z == 0) { z = 1; } } #ifdef DEBUG_RNPXLSEARCH cout << "after deisotoping..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; -// for (Size i = 0; i != exp[exp_index].size(); ++i) cout << exp[exp_index][i].getMZ() << "\t" << exp[exp_index][i].getIntensity() << endl; cout << "Fragment charges in spectrum: " << exp_index << endl; - if (exp[exp_index].getIntegerDataArrays().size()) - for (Size i = 0; i != exp[exp_index].size(); ++i) - cout << exp[exp_index][i].getMZ() << "\t" << exp[exp_index][i].getIntensity() << "\t" << exp[exp_index].getIntegerDataArrays()[0][i] << endl; + if (spec.getIntegerDataArrays().size()) + for (Size i = 0; i != spec.size(); ++i) + cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << "\t" << ia[i] << endl; cout << endl; #endif // remove noise - window_mower_filter.filterPeakSpectrum(exp[exp_index]); + window_mower_filter.filterPeakSpectrum(spec); #ifdef DEBUG_RNPXLSEARCH cout << "after mower..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; - for (Size i = 0; i != exp[exp_index].size(); ++i) cout << exp[exp_index][i].getMZ() << "\t" << exp[exp_index][i].getIntensity() << endl; + for (Size i = 0; i != spec.size(); ++i) cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << endl; cout << "Fragment charges in spectrum: " << exp_index << endl; - if (exp[exp_index].getIntegerDataArrays().size()) - for (Size i = 0; i != exp[exp_index].size(); ++i) - cout << exp[exp_index][i].getMZ() << "\t" << exp[exp_index][i].getIntensity() << "\t" << exp[exp_index].getIntegerDataArrays()[0][i] << endl; + if (spec.getIntegerDataArrays().size()) + for (Size i = 0; i != spec.size(); ++i) + cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << "\t" << ia[i] << endl; #endif - nlargest_filter.filterPeakSpectrum(exp[exp_index]); + nlargest_filter.filterPeakSpectrum(spec); #ifdef DEBUG_RNPXLSEARCH cout << "after nlargest..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; - for (Size i = 0; i != exp[exp_index].size(); ++i) cout << exp[exp_index][i].getMZ() << "\t" << exp[exp_index][i].getIntensity() << endl; + for (Size i = 0; i != spec.size(); ++i) cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << endl; cout << "Fragment charges in spectrum: " << exp_index << endl; - if (exp[exp_index].getIntegerDataArrays().size()) - for (Size i = 0; i != exp[exp_index].size(); ++i) - cout << exp[exp_index][i].getMZ() << "\t" << exp[exp_index][i].getIntensity() << "\t" << exp[exp_index].getIntegerDataArrays()[0][i] << endl; + if (spec.getIntegerDataArrays().size()) + for (Size i = 0; i != spec.size(); ++i) + cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << "\t" << ia[i] << endl; #endif // sort (nlargest changes order) - exp[exp_index].sortByPosition(); + spec.sortByPosition(); #ifdef DEBUG_RNPXLSEARCH cout << "after sort..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; - for (Size i = 0; i != exp[exp_index].size(); ++i) cout << exp[exp_index][i].getMZ() << "\t" << exp[exp_index][i].getIntensity() << endl; - if (exp[exp_index].getIntegerDataArrays().size()) - for (Size i = 0; i != exp[exp_index].size(); ++i) - cout << exp[exp_index][i].getMZ() << "\t" << exp[exp_index][i].getIntensity() << "\t" << exp[exp_index].getIntegerDataArrays()[0][i] << endl; + for (Size i = 0; i != spec.size(); ++i) cout << spec[i].getMZ() << "\t" << spec.getIntensity() << endl; + if (spec.getIntegerDataArrays().size()) + for (Size i = 0; i != spec.size(); ++i) + cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << "\t" << ia[i] << endl; #endif } @@ -766,8 +772,8 @@ class RNPxlSearch : if (loss_first != string::npos) // ion with neutral loss e.g. water { - // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + // only allow matching charges + if (fragment_charge == charge) { PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; @@ -789,7 +795,7 @@ class RNPxlSearch : peak_is_annotated.insert(aligned.second); // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + if (fragment_charge == charge) { RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); unshifted_y_ions[ion_number].push_back(d); @@ -809,8 +815,8 @@ class RNPxlSearch : if (loss_first != string::npos) { - // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + // only allow matching charges + if (fragment_charge == charge) { PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; @@ -832,7 +838,7 @@ class RNPxlSearch : peak_is_annotated.insert(aligned.second); // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + if (fragment_charge == charge) { RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); unshifted_b_ions[ion_number].push_back(d); @@ -853,7 +859,7 @@ class RNPxlSearch : if (loss_first != string::npos) { // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + if (fragment_charge == charge) { PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; @@ -875,7 +881,7 @@ class RNPxlSearch : peak_is_annotated.insert(aligned.second); // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + if (fragment_charge == charge) { RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); unshifted_a_ions[ion_number].push_back(d); @@ -988,8 +994,8 @@ class RNPxlSearch : ion_nr_string.substitute("+", ""); // remove one or multiple '+' auto ion_number = (Size)ion_nr_string.toInt(); - // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + // only allow matching charges + if (fragment_charge == charge) { RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); shifted_y_ions[ion_number].push_back(d); @@ -1008,8 +1014,8 @@ class RNPxlSearch : ion_nr_string.substitute("+", ""); // remove one or multiple '+' auto ion_number = (Size)ion_nr_string.toInt(); - // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + // only allow matching charges + if (fragment_charge == charge) { RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); shifted_b_ions[ion_number].push_back(d); @@ -1029,7 +1035,7 @@ class RNPxlSearch : auto ion_number = (Size)ion_nr_string.toInt(); // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == 0 || fragment_charge == charge) + if (fragment_charge == charge) { RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); shifted_a_ions[ion_number].push_back(d); @@ -1043,7 +1049,7 @@ class RNPxlSearch : } else if (ion_name.hasPrefix(ANNOTATIONS_MARKER_ION_PREFIX)) { - if (fragment_charge <= 1) + if (fragment_charge == 1) { PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; @@ -1061,7 +1067,7 @@ class RNPxlSearch : } else if (ion_name.hasPrefix("i")) { - if (fragment_charge <= 1) + if (fragment_charge == 1) { PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; From fdc4fa6dcb76f0feb84ad09f93bbb032445d8987 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 5 Feb 2019 11:13:49 +0100 Subject: [PATCH 003/471] [FIX] only match peaks matching in charge --- .../OpenMS/ANALYSIS/RNPXL/HyperScore.h | 23 ++- .../source/ANALYSIS/RNPXL/HyperScore.cpp | 88 +++++++++++ src/tests/topp/RNPxlSearch_1_output.idXML | 138 +++++++++--------- src/tests/topp/RNPxlSearch_2_output.idXML | 138 +++++++++--------- src/tests/topp/RNPxlSearch_3_output.idXML | 96 ++++++------ src/tests/topp/RNPxlSearch_3_output2.tsv | 24 +-- src/tests/topp/RNPxlSearch_4_output.idXML | 114 +++++++-------- src/tests/topp/RNPxlSearch_4_output2.tsv | 28 ++-- src/utils/RNPxlSearch.cpp | 59 +++++--- 9 files changed, 421 insertions(+), 287 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h index 70e907b80af..b25d5c60dc7 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h @@ -37,6 +37,7 @@ #include #include #include +#include #include namespace OpenMS @@ -61,7 +62,27 @@ struct OPENMS_DLLAPI HyperScore */ // static double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const RichPeakSpectrum& theo_spectrum); - static double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum); + static double compute(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const PeakSpectrum& theo_spectrum); + /* @brief compute the (ln transformed) X!Tandem HyperScore only matching peaks that match in charge + * 1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated + * 2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions + * @note Peak intensities of the theoretical spectrum are typically 1 or TIC normalized, but can also be e.g. ion probabilities + * @param fragment_mass_tolerance mass tolerance applied left and right of the theoretical spectrum peak position + * @param fragment_mass_tolerance_unit_ppm Unit of the mass tolerance is: Thomson if false, ppm if true + * @param exp_spectrum measured spectrum + * @param exp_charges charges of measured peaks + * @param theo_spectrum theoretical spectrum Peaks need to contain an ion annotation as provided by TheoreticalSpectrumGenerator. + * @param theo_charges charges of theoretical peaks + */ + static double compute(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const DataArrays::IntegerDataArray& exp_charges, + const PeakSpectrum& theo_spectrum, + const DataArrays::IntegerDataArray& theo_charges); private: // helper to compute the log factorial diff --git a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp index 4dcf5b0c39f..419bd319e78 100644 --- a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp @@ -114,5 +114,93 @@ namespace OpenMS return hyperScore; } + double HyperScore::compute(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const DataArrays::IntegerDataArray& exp_charges, + const PeakSpectrum& theo_spectrum, + const DataArrays::IntegerDataArray& theo_charges) + { + double dot_product = 0.0; + UInt y_ion_count = 0; + UInt b_ion_count = 0; + + if (exp_spectrum.size() < 1 || theo_spectrum.size() < 1) + { + std::cout << "Warning: HyperScore: One of the given spectra is empty." << std::endl; + return 0.0; + } + + // TODO this assumes only one StringDataArray is present and it is the right one + const PeakSpectrum::StringDataArray* ion_names; + if (theo_spectrum.getStringDataArrays().size() > 0) + { + ion_names = &theo_spectrum.getStringDataArrays()[0]; + } + else + { + std::cout << "Error: HyperScore: Theoretical spectrum without StringDataArray (\"IonNames\" annotation) provided." << std::endl; + return 0.0; + } + + if (theo_charges.size() != theo_spectrum.size()) + { + std::cout << "Error: HyperScore: #charges != #peaks in theoretical spectrum." << std::endl; + return 0.0; + } + + if (exp_charges.size() != exp_spectrum.size()) + { + std::cout << "Error: HyperScore: #charges != #peaks in experimental spectrum." << std::endl; + return 0.0; + } + + for (Size i = 0; i < theo_spectrum.size(); ++i) + { + const double theo_mz = theo_spectrum[i].getMZ(); + + double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + + // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak + Size index = exp_spectrum.findNearest(theo_mz); + + const double exp_mz = exp_spectrum[index].getMZ(); + const double theo_intensity = theo_spectrum[i].getIntensity(); + const int exp_z = exp_charges[index]; + const int theo_z = theo_charges[i]; + + #ifdef DEBUG_HYPERSCORE + if (exp_z != theo_z) std::cout << "exp_z != theo_z " << exp_z << "\t" << theo_z << std::endl; + #endif + + // found peak match + if (std::abs(theo_mz - exp_mz) < max_dist_dalton + && exp_z == theo_z) + { + dot_product += exp_spectrum[index].getIntensity() * theo_intensity /* * mass_error */; + // fragment annotations in XL-MS data are more complex and do not start with the ion type, but the ion type always follows after a $ + if ((*ion_names)[i][0] == 'y' || (*ion_names)[i].hasSubstring("$y")) + { + #ifdef DEBUG_HYPERSCORE + std::cout << (*ion_names)[i] << " intensity: " << exp_spectrum[index].getIntensity() << std::endl; + #endif + ++y_ion_count; + } + else if ((*ion_names)[i][0] == 'b' || (*ion_names)[i].hasSubstring("$b")) + { + #ifdef DEBUG_HYPERSCORE + std::cout << (*ion_names)[i] << " intensity: " << exp_spectrum[index].getIntensity() << std::endl; + #endif + ++b_ion_count; + } + } + } + + const double yFact = logfactorial_(y_ion_count); + const double bFact = logfactorial_(b_ion_count); + const double hyperScore = log1p(dot_product) + yFact + bFact; + return hyperScore; + } + } diff --git a/src/tests/topp/RNPxlSearch_1_output.idXML b/src/tests/topp/RNPxlSearch_1_output.idXML index c964a288557..548c0b38284 100644 --- a/src/tests/topp/RNPxlSearch_1_output.idXML +++ b/src/tests/topp/RNPxlSearch_1_output.idXML @@ -6,7 +6,7 @@ - + @@ -26,7 +26,7 @@ - + @@ -45,7 +45,7 @@ - + @@ -73,7 +73,7 @@ - + @@ -91,8 +91,8 @@ - - + + @@ -119,10 +119,10 @@ - - - - + + + + @@ -138,8 +138,8 @@ - - + + @@ -167,7 +167,7 @@ - + @@ -214,7 +214,7 @@ - + @@ -260,10 +260,10 @@ - - - - + + + + @@ -279,9 +279,9 @@ - - - + + + @@ -308,7 +308,7 @@ - + @@ -343,8 +343,8 @@ - - + + @@ -355,7 +355,7 @@ - + @@ -373,8 +373,8 @@ - - + + @@ -402,7 +402,7 @@ - + @@ -420,8 +420,8 @@ - - + + @@ -449,7 +449,7 @@ - + @@ -496,7 +496,7 @@ - + @@ -514,8 +514,8 @@ - - + + @@ -543,7 +543,7 @@ - + @@ -561,8 +561,8 @@ - - + + @@ -590,7 +590,7 @@ - + @@ -608,8 +608,8 @@ - - + + @@ -684,7 +684,7 @@ - + @@ -702,8 +702,8 @@ - - + + @@ -730,27 +730,27 @@ - - - + + + - + - + - + - + - + - - + + @@ -766,8 +766,8 @@ - - + + @@ -778,7 +778,7 @@ - + @@ -825,7 +825,7 @@ - + @@ -843,8 +843,8 @@ - - + + @@ -871,10 +871,10 @@ - - - - + + + + @@ -890,8 +890,8 @@ - - + + @@ -918,10 +918,10 @@ - - - - + + + + diff --git a/src/tests/topp/RNPxlSearch_2_output.idXML b/src/tests/topp/RNPxlSearch_2_output.idXML index 03eaddef77a..21561ef0893 100644 --- a/src/tests/topp/RNPxlSearch_2_output.idXML +++ b/src/tests/topp/RNPxlSearch_2_output.idXML @@ -6,7 +6,7 @@ - + @@ -26,7 +26,7 @@ - + @@ -45,7 +45,7 @@ - + @@ -74,7 +74,7 @@ - + @@ -92,8 +92,8 @@ - - + + @@ -122,9 +122,9 @@ - - - + + + @@ -140,8 +140,8 @@ - - + + @@ -163,14 +163,14 @@ - + - + @@ -218,7 +218,7 @@ - + @@ -266,9 +266,9 @@ - - - + + + @@ -284,9 +284,9 @@ - - - + + + @@ -307,14 +307,14 @@ - + - + @@ -349,8 +349,8 @@ - - + + @@ -362,7 +362,7 @@ - + @@ -380,8 +380,8 @@ - - + + @@ -410,7 +410,7 @@ - + @@ -428,8 +428,8 @@ - - + + @@ -458,7 +458,7 @@ - + @@ -506,7 +506,7 @@ - + @@ -524,8 +524,8 @@ - - + + @@ -554,7 +554,7 @@ - + @@ -572,8 +572,8 @@ - - + + @@ -602,7 +602,7 @@ - + @@ -620,8 +620,8 @@ - - + + @@ -698,7 +698,7 @@ - + @@ -716,8 +716,8 @@ - - + + @@ -746,26 +746,26 @@ - - + + - + - + - + - + - + - - + + @@ -781,20 +781,20 @@ - - + + - + - + @@ -842,7 +842,7 @@ - + @@ -860,8 +860,8 @@ - - + + @@ -890,9 +890,9 @@ - - - + + + @@ -908,8 +908,8 @@ - - + + @@ -931,16 +931,16 @@ - + - - - + + + @@ -979,7 +979,7 @@ - + diff --git a/src/tests/topp/RNPxlSearch_3_output.idXML b/src/tests/topp/RNPxlSearch_3_output.idXML index 131f00d694a..125044ce299 100644 --- a/src/tests/topp/RNPxlSearch_3_output.idXML +++ b/src/tests/topp/RNPxlSearch_3_output.idXML @@ -5,7 +5,7 @@ - + @@ -25,7 +25,7 @@ - + @@ -43,8 +43,8 @@ - - + + @@ -115,7 +115,7 @@ - + @@ -133,8 +133,8 @@ - - + + @@ -162,7 +162,7 @@ - + @@ -180,8 +180,8 @@ - - + + @@ -209,7 +209,7 @@ - + @@ -345,10 +345,10 @@ - - - - + + + + @@ -389,7 +389,7 @@ - + @@ -436,7 +436,7 @@ - + @@ -483,7 +483,7 @@ - + @@ -501,8 +501,8 @@ - - + + @@ -526,7 +526,7 @@ - + @@ -573,7 +573,7 @@ - + @@ -591,8 +591,8 @@ - - + + @@ -667,7 +667,7 @@ - + @@ -685,8 +685,8 @@ - - + + @@ -808,7 +808,7 @@ - + @@ -855,7 +855,7 @@ - + @@ -873,8 +873,8 @@ - - + + @@ -902,7 +902,7 @@ - + @@ -920,8 +920,8 @@ - - + + @@ -949,7 +949,7 @@ - + @@ -1039,7 +1039,7 @@ - + @@ -1057,8 +1057,8 @@ - - + + @@ -1085,10 +1085,10 @@ - - - - + + + + @@ -1104,8 +1104,8 @@ - - + + @@ -1132,10 +1132,10 @@ - - - - + + + + diff --git a/src/tests/topp/RNPxlSearch_3_output2.tsv b/src/tests/topp/RNPxlSearch_3_output2.tsv index 44724342a56..654b505cd9f 100644 --- a/src/tests/topp/RNPxlSearch_3_output2.tsv +++ b/src/tests/topp/RNPxlSearch_3_output2.tsv @@ -1,26 +1,26 @@ #RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.06231 A_330.06033 C_112.05108 C_306.0491 G_152.05723 G_346.05525 U_113.03509 U_307.03311 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank -17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 7.69674253463745 3.28702163696289 0 0 16.86 0 0 7.87 0 0 0 328.70 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 +17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 7.69674253463745 3.20641875267029 0 0 16.86 0 0 7.87 0 0 0 320.64 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 17.788 712.7828 Cas6e UU-H2O1 LRANPIK 2 0.090044192969799 0 0 0 0 0 0 0 0 LRANPIK 810.5076 612.0506 1422.5582 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.4965 697.0 1423.5655 712.2864 475.1933 356.6468 2 -18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.68516635894775 2.3846275806427 0 0 0 238.46 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 -25.116 508.1855 Cas5 AU YTPYLGR 3 2.28572154045105 0.594124555587769 0 0 0 59.41 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 +18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.68516635894775 2.21110057830811 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 +25.116 508.1855 Cas5 AU YTPYLGR 3 2.28572154045105 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 26.237 678.2844 Cas5 U DYHTVLGAR 2 12.1896953582764 0.0519835986196995 0 5.20 0 0 0 0 0 0 0 DyHTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 18.437629699707 0.253752440214157 25.38 21.64 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 26.413 791.8590 Cas5 CU-H2O1-H1O3P1 MRSYLILR 2 0.113123878836632 0 0 0 0 0 0 0 0 0 MRSYLILR 1050.6008 531.1003 1581.7011 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0012 1.5 1582.7084 791.8578 528.2410 396.4325 2 -28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 14.8608360290527 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 +28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.0651416778564 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 28.487 828.6961 Cas5 CU-H2O1-H1O3P1 DDTSSLQALSESVQFAVR 3 1.20521605014801 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 DDTSSLQALSESVQFAVR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.97172045707703 0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 -31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.32002639770508 5.09459018707275 0 0 0 0 20.82 0 0 0 0 509.46 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 +31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.32002639770508 5.02087736129761 0 0 0 0 0 0 0 0 0 502.09 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 31.812 957.3968 Cse2 GU-H2O1-H1O3P1 LVQPFGWENPR 2 0.699610769748688 0 0 0 0 0 0 0 0 0 0 0 0 LVQPFGWENPR 1341.6830 571.1064 1912.7894 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 0.0052 -5.4 1913.7967 957.4020 638.6037 479.2046 2 -33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74696397781372 3.97626733779907 0 0 397.63 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 +33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74696397781372 3.93728351593018 0 0 393.73 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 9.35551738739014 0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 -34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7018890380859 3.28482103347778 328.48 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 +34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7018890380859 3.19935750961304 319.94 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 34.072 648.2559 Cas5 UU-H2O1 AVLKPR 2 0.141841292381287 0 0 0 0 0 0 0 AVLKPR 682.4490 612.0506 1294.4996 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0012 -1.8 1295.5069 648.2571 432.5071 324.6322 1 36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 13.1162643432617 2.20912766456604 0 0 0 0 0 0 220.91 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 9.67764759063721 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 -37.098 735.8139 Cse1 U ALYTFAEGFK 2 13.8854703903198 1.44568836688995 35.65 0 0 0 115.17 125.30 0 144.57 0 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 -37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.48794269561768 4.26199531555176 0 0 0 0 0 0 426.20 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 +37.098 735.8139 Cse1 U ALYTFAEGFK 2 13.8854703903198 1.3745938539505 16.33 0 0 0 105.82 118.19 0 137.46 0 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 +37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.48794269561768 4.0868239402771 0 0 0 0 0 0 408.68 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 37.864 698.2974 Cas5 U DEPMITLPR 2 10.3223762512207 0.18551279604435 0 0 18.55 0 0 0 0 11.57 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 37.864 698.2974 Cas7 CU-H2O1-H1O3P1 DAIFGGKR 2 0.214722290635109 0 0 0 0 0 0 0 0 0 DAIFGGKR 862.4661 531.1003 1393.5664 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.5069 726.4 1394.5736 697.7905 465.5294 349.3989 2 -39.118 623.2540 Cse2 U MLTWWGK 2 3.63084125518799 0.968599498271942 0 0 0 96.86 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 -39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 12.5546894073486 1.48393821716309 29.06 0 0 15.05 0 0 0 0 148.39 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 -40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 6.28417921066284 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 +39.118 623.2540 Cse2 U MLTWWGK 2 3.63084125518799 0.95687198638916 0 0 0 95.69 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 +39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 8.496826171875 1.10095739364624 0 0 0 0 0 0 0 0 110.10 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 +40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 4.66531610488892 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 diff --git a/src/tests/topp/RNPxlSearch_4_output.idXML b/src/tests/topp/RNPxlSearch_4_output.idXML index 5095763dbf9..ddf7462a2a9 100644 --- a/src/tests/topp/RNPxlSearch_4_output.idXML +++ b/src/tests/topp/RNPxlSearch_4_output.idXML @@ -5,7 +5,7 @@ - + @@ -37,7 +37,7 @@ - + @@ -55,8 +55,8 @@ - - + + @@ -129,7 +129,7 @@ - + @@ -147,8 +147,8 @@ - - + + @@ -177,7 +177,7 @@ - + @@ -195,8 +195,8 @@ - - + + @@ -225,7 +225,7 @@ - + @@ -409,9 +409,9 @@ - - - + + + @@ -450,12 +450,12 @@ - + - - - + + + @@ -471,8 +471,8 @@ - - + + @@ -494,14 +494,14 @@ - + - + @@ -549,7 +549,7 @@ - + @@ -567,8 +567,8 @@ - - + + @@ -593,7 +593,7 @@ - + @@ -641,7 +641,7 @@ - + @@ -659,8 +659,8 @@ - - + + @@ -685,7 +685,7 @@ - + @@ -703,8 +703,8 @@ - - + + @@ -781,7 +781,7 @@ - + @@ -799,8 +799,8 @@ - - + + @@ -969,7 +969,7 @@ - + @@ -1061,7 +1061,7 @@ - + @@ -1079,8 +1079,8 @@ - - + + @@ -1153,7 +1153,7 @@ - + @@ -1171,8 +1171,8 @@ - - + + @@ -1201,7 +1201,7 @@ - + @@ -1293,7 +1293,7 @@ - + @@ -1311,8 +1311,8 @@ - - + + @@ -1341,9 +1341,9 @@ - - - + + + @@ -1359,8 +1359,8 @@ - - + + @@ -1382,10 +1382,10 @@ - + - + @@ -1433,9 +1433,9 @@ - - - + + + @@ -1474,7 +1474,7 @@ - + diff --git a/src/tests/topp/RNPxlSearch_4_output2.tsv b/src/tests/topp/RNPxlSearch_4_output2.tsv index 48c748a9903..bb9ab205aa6 100644 --- a/src/tests/topp/RNPxlSearch_4_output2.tsv +++ b/src/tests/topp/RNPxlSearch_4_output2.tsv @@ -1,32 +1,32 @@ #RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.06231 A_330.06033 C_112.05108 C_306.0491 G_152.05723 G_346.05525 U_113.03509 U_307.03311 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank -17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 7.69674253463745 3.28702163696289 0 0 16.86 0 0 7.87 0 0 0 328.70 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 +17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 7.69674253463745 3.20641875267029 0 0 16.86 0 0 7.87 0 0 0 320.64 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 17.788 712.7828 DECOY_Cas7 U-H2O1 KDDLNDAEAK 2 1.92921662330627 0.278845310211182 27.88 25.57 23.13 0 0 0 0 0 0 0 kDDLNDAEAK 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 2 -18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.68516635894775 2.3846275806427 0 0 0 238.46 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 -25.116 508.1855 Cas5 AU YTPYLGR 3 2.28572154045105 0.594124555587769 0 0 0 59.41 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 +18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.68516635894775 2.21110057830811 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 +25.116 508.1855 Cas5 AU YTPYLGR 3 2.28572154045105 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 26.237 678.2844 Cas5 U DYHTVLGAR 2 12.1896953582764 0.0519835986196995 0 5.20 0 0 0 0 0 0 0 DyHTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 26.237 678.2844 DECOY_Cas5 U AGLVTHYDR 2 0.300964891910553 0.0519835986196995 0 0 0 0 0 0 5.20 0 0 AGLVTHyDR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 2 26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 18.437629699707 0.253752440214157 25.38 21.64 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 26.413 791.8590 Cas5 CU-H2O1-H1O3P1 MRSYLILR 2 0.113123878836632 0 0 0 0 0 0 0 0 0 MRSYLILR 1050.6008 531.1003 1581.7011 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0012 1.5 1582.7084 791.8578 528.2410 396.4325 2 -28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 14.8608360290527 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 -28.487 828.6961 DECOY_Cas5 CU-H2O1-H1O3P1 VAFQVSESLAQLSSTDDR 3 1.21729958057404 0.954662799835205 95.47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 vAFQVSESLAQLSSTDDR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 +28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.0651416778564 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 +28.487 828.6961 DECOY_Cas5 CU-H2O1-H1O3P1 VAFQVSESLAQLSSTDDR 3 1.21061110496521 0.936702311038971 93.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 vAFQVSESLAQLSSTDDR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.97172045707703 0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 -31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.32002639770508 5.09459018707275 0 0 0 0 20.82 0 0 0 0 509.46 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 +31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.32002639770508 5.02087736129761 0 0 0 0 0 0 0 0 0 502.09 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 31.812 957.3968 DECOY_Cse2 U IQACSGNDLQQWAR 2 1.43600630760193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 IQACSGNDLQQWAR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 2 -33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74696397781372 3.97626733779907 0 0 397.63 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 -33.237 510.2805 DECOY_Cas7 U-H2O1 LVKLLK 2 1.40568971633911 1.07130634784698 0 0 107.13 0 0 0 LVkLLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 +33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74696397781372 3.93728351593018 0 0 393.73 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 +33.237 510.2805 DECOY_Cas7 U-H2O1 LVKLLK 2 1.40568971633911 1.03232252597809 0 0 103.23 0 0 0 LVkLLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 9.35551738739014 0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 -34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7018890380859 3.28482103347778 328.48 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 +34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7018890380859 3.19935750961304 319.94 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 34.072 648.2559 Cas5 UU-H2O1 AVLKPR 2 0.141841292381287 0 0 0 0 0 0 0 AVLKPR 682.4490 612.0506 1294.4996 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0012 -1.8 1295.5069 648.2571 432.5071 324.6322 1 36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 13.1162643432617 2.20912766456604 0 0 0 0 0 0 220.91 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 36.528 938.3693 DECOY_Cse1 AU-H2O1 GNSPGGQPKLER 2 0.224538460373878 0 0 0 0 0 0 0 0 0 0 0 0 0 GNSPGGQPKLER 1238.6368 635.0778 1873.7146 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.5047 538.1 1874.7219 937.8646 625.5788 469.4359 2 36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 9.67764759063721 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 36.767 933.9406 DECOY_Cas7 U-H2O1 EAEDVSKGSLLALTK 2 0.208499565720558 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 EAEDVSKGSLLALTK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 2 -37.098 735.8139 Cse1 U ALYTFAEGFK 2 13.8854703903198 1.44568836688995 35.65 0 0 0 115.17 125.30 0 144.57 0 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 +37.098 735.8139 Cse1 U ALYTFAEGFK 2 13.8854703903198 1.3745938539505 16.33 0 0 0 105.82 118.19 0 137.46 0 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 0.31612566113472 0 0 0 0 0 0 0 0 0 0 0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 -37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.48794269561768 4.26199531555176 0 0 0 0 0 0 426.20 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 +37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.48794269561768 4.0868239402771 0 0 0 0 0 0 408.68 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 37.864 698.2974 Cas5 U DEPMITLPR 2 10.3223762512207 0.18551279604435 0 0 18.55 0 0 0 0 11.57 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 37.864 698.2974 Cas7 CU-H2O1-H1O3P1 DAIFGGKR 2 0.214722290635109 0 0 0 0 0 0 0 0 0 DAIFGGKR 862.4661 531.1003 1393.5664 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.5069 726.4 1394.5736 697.7905 465.5294 349.3989 2 -39.118 623.2540 Cse2 U MLTWWGK 2 3.63084125518799 0.968599498271942 0 0 0 96.86 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 -39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 12.5546894073486 1.48393821716309 29.06 0 0 15.05 0 0 0 0 148.39 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 +39.118 623.2540 Cse2 U MLTWWGK 2 3.63084125518799 0.95687198638916 0 0 0 95.69 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 +39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 8.496826171875 1.10095739364624 0 0 0 0 0 0 0 0 110.10 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 39.853 861.3889 DECOY_Cas5 U GTPRTGEFTPQGWAQMPGALR 3 2.99082112312317 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 GTPRTGEFTPQGWAQMPGALR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 2 -40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 6.28417921066284 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 +40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 4.66531610488892 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 6c02e07afb9..e65d2ac9a39 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -395,7 +395,11 @@ class RNPxlSearch : /* @brief Filter spectra to remove noise. Parameter are passed to spectra filter. */ - void preprocessSpectra_(PeakMap& exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool annotate_charge = false) + void preprocessSpectra_(PeakMap& exp, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + bool single_charge_spectra, + bool annotate_charge = false) { // filter MS2 map // remove 0 intensities @@ -436,10 +440,13 @@ class RNPxlSearch : single_charge_spectra, annotate_charge); - // set Unknown charge to z=1. Otherwise we get a lot of spurious matches - // to highly charged fragments in the low m/z region - DataArrays::IntegerDataArray& ia = spec.getIntegerDataArrays()[0]; // charge array - for (int & z : ia) { if (z == 0) { z = 1; } } + if (annotate_charge) + { + // set Unknown charge to z=1. Otherwise we get a lot of spurious matches + // to highly charged fragments in the low m/z region + DataArrays::IntegerDataArray& ia = spec.getIntegerDataArrays()[0]; // charge array + for (int & z : ia) { if (z == 0) { z = 1; } } + } #ifdef DEBUG_RNPXLSEARCH cout << "after deisotoping..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; @@ -487,8 +494,6 @@ class RNPxlSearch : cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << "\t" << ia[i] << endl; #endif } - -// MzMLFile().store(String("RNPxlSearch_a_") + String((int)annotate_charge) + ".mzML", exp); } @@ -1723,8 +1728,12 @@ class RNPxlSearch : progresslogger.startProgress(0, 1, "Filtering spectra..."); const bool convert_to_single_charge = false; // whether to convert fragment peaks with isotopic patterns to single charge - const bool annotate_charge = false; // whether the charge and type is annotated - preprocessSpectra_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, convert_to_single_charge, annotate_charge); + const bool annotate_charge = true; + preprocessSpectra_(spectra, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + convert_to_single_charge, // no single charge (false), annotate charge (true) + annotate_charge); progresslogger.endProgress(); // build multimap of precursor mass to scan index (and perform some mass and length based filtering) @@ -1755,7 +1764,7 @@ class RNPxlSearch : for (auto & a : annotated_hits) { a.reserve(2 * report_top_hits); } #ifdef _OPENMP - // we want to do locking at the spectrum level so we get good parallelisation + // locking is done at the spectrum level to ensure good parallelisation vector annotated_hits_lock(annotated_hits.size()); for (size_t i = 0; i != annotated_hits_lock.size(); i++) { omp_init_lock(&(annotated_hits_lock[i])); } #endif @@ -2273,7 +2282,11 @@ class RNPxlSearch : spectra.sortSpectra(true); // for post scoring don't convert fragments to single charge. Annotate charge instead to every peak. - preprocessSpectra_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, false, true); // no single charge (false), annotate charge (true) + preprocessSpectra_(spectra, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + false, // no single charge (false), annotate charge (true) + true); progresslogger.startProgress(0, 1, "localization..."); @@ -2386,8 +2399,12 @@ class RNPxlSearch : float &precursor_sub_score, float &a_ion_sub_score) const { - total_loss_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - exp_spectrum, total_loss_spectrum); + total_loss_score = HyperScore::compute(fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + total_loss_spectrum, + total_loss_spectrum.getIntegerDataArrays()[0]); // bad score, likely wihout any single matching peak if (total_loss_score < 0.01) { return; } @@ -2467,8 +2484,12 @@ class RNPxlSearch : { if (exp_pc_charge < 3) { - partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - exp_spectrum, partial_loss_spectrum_z1); + partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + partial_loss_spectrum_z1, + partial_loss_spectrum_z1.getIntegerDataArrays()[0]); auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, @@ -2480,8 +2501,12 @@ class RNPxlSearch : } else //if (exp_pc_charge >= 3) { - partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - exp_spectrum, partial_loss_spectrum_z2); + partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + partial_loss_spectrum_z2, + partial_loss_spectrum_z2.getIntegerDataArrays()[0]); auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, From 2d10e10cfe8ff492d6a8920ef90f109561ec9f2e Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 5 Feb 2019 14:10:02 +0100 Subject: [PATCH 004/471] [FEATURE] changed defaults, make morpheus score charge aware --- .../OpenMS/ANALYSIS/RNPXL/MorpheusScore.h | 9 + .../source/ANALYSIS/RNPXL/MorpheusScore.cpp | 93 +++ .../TheoreticalSpectrumGenerator.cpp | 41 +- src/tests/topp/RNPxlSearch_1_output.idXML | 80 +- src/tests/topp/RNPxlSearch_2_output.idXML | 80 +- src/tests/topp/RNPxlSearch_3_output.idXML | 563 ++++++++------ src/tests/topp/RNPxlSearch_3_output2.tsv | 52 +- src/tests/topp/RNPxlSearch_4_output.idXML | 713 ++++++++++-------- src/tests/topp/RNPxlSearch_4_output2.tsv | 63 +- src/utils/RNPxlSearch.cpp | 67 +- 10 files changed, 1026 insertions(+), 735 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/MorpheusScore.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/MorpheusScore.h index e3385ad3d7c..fee2ebd1b04 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/MorpheusScore.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/MorpheusScore.h @@ -37,6 +37,7 @@ #include #include #include +#include namespace OpenMS { @@ -64,6 +65,14 @@ struct OPENMS_DLLAPI MorpheusScore bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum); + + /// same as above but matches are only counted if charges match + static Result compute(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const DataArrays::IntegerDataArray& exp_charges, + const PeakSpectrum& theo_spectrum, + const DataArrays::IntegerDataArray& theo_charges); }; } diff --git a/src/openms/source/ANALYSIS/RNPXL/MorpheusScore.cpp b/src/openms/source/ANALYSIS/RNPXL/MorpheusScore.cpp index b9ea27381d8..1ac84abe12c 100644 --- a/src/openms/source/ANALYSIS/RNPXL/MorpheusScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/MorpheusScore.cpp @@ -116,5 +116,98 @@ namespace OpenMS psm.err = matches > 0 ? sum_error / static_cast(matches) : 1e10; return psm; } + + MorpheusScore::Result MorpheusScore::compute(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const DataArrays::IntegerDataArray& exp_charges, + const PeakSpectrum& theo_spectrum, + const DataArrays::IntegerDataArray& theo_charges) + + { + const Size n_t(theo_spectrum.size()); + const Size n_e(exp_spectrum.size()); + + MorpheusScore::Result psm = {}; + + if (n_t == 0 || n_e == 0) { return psm; } + + Size t(0), e(0), matches(0); + double total_intensity(0); + + // count matching peaks and make sure that every theoretical peak is matched at most once + while (t < n_t && e < n_e) + { + const double theo_mz = theo_spectrum[t].getMZ(); + const double exp_mz = exp_spectrum[e].getMZ(); + const double d = exp_mz - theo_mz; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + if (fabs(d) <= max_dist_dalton) // match in tolerance window? + { + const int exp_charge(exp_charges[e]); + const int theo_charge(theo_charges[t]); + if (exp_charge == theo_charge) + { + ++matches; + } + ++t; // count theoretical peak only once + } + else if (d < 0) // exp. peak is left of theo. peak (outside of tolerance window) + { + total_intensity += exp_spectrum[e].getIntensity(); + ++e; + } + else if (d > 0) // theo. peak is left of exp. peak (outside of tolerance window) + { + ++t; + } + } + + for (; e < n_e; ++e) { total_intensity += exp_spectrum[e].getIntensity(); } + + // similar to above but we now make sure that the intensity of every matched experimental peak is summed up to form match_intensity + t = 0; + e = 0; + double match_intensity(0.0); + double sum_error(0.0); + + while (t < n_t && e < n_e) + { + const double theo_mz = theo_spectrum[t].getMZ(); + const double exp_mz = exp_spectrum[e].getMZ(); + const double d = exp_mz - theo_mz; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + if (fabs(d) <= max_dist_dalton) // match in tolerance window? + { + const int exp_charge(exp_charges[e]); + const int theo_charge(theo_charges[t]); + if (exp_charge == theo_charge) + { + match_intensity += exp_spectrum[e].getIntensity(); + sum_error += fabs(d); + } + ++e; // sum up experimental peak intensity only once + } + else if (d < 0) // exp. peak is left of theo. peak (outside of tolerance window) + { + ++e; + } + else if (d > 0) // theo. peak is left of exp. peak (outside of tolerance window) + { + ++t; + } + } + + const double intensity_fraction = match_intensity / total_intensity; + + psm.score = static_cast(matches) + intensity_fraction; + psm.n_peaks = theo_spectrum.size(); + psm.matches = matches; + psm.MIC = match_intensity; + psm.TIC = total_intensity; + psm.err = matches > 0 ? sum_error / static_cast(matches) : 1e10; + return psm; + } + } diff --git a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp index 1199dfd7a6f..0d810584501 100644 --- a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp +++ b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp @@ -555,7 +555,15 @@ namespace OpenMS { Peak1D p; - String ion_name("[M+H]" + String((Size)charge, '+')); + String ion_name; + if (charge == 1) + { + ion_name = "[M+H]+"; + } + else + { + ion_name = "[M+" + String(charge) + "H]" + String(charge) + "+"; + } // precursor peak double mono_pos = peptide.getMonoWeight(Residue::Full, charge); @@ -602,7 +610,15 @@ namespace OpenMS p.setIntensity(pre_int_H2O_ * it->getIntensity()); if (add_metainfo_) { - String ion_name("[M+H]-H2O" + String((Size)charge, '+')); + String ion_name; + if (charge == 1) + { + ion_name = "[M+H-H2O]+"; + } + else + { + ion_name = "[M+" + String(charge) + "H-H2O]" + String(charge) + "+"; + } ion_names.push_back(ion_name); charges.push_back(charge); } @@ -635,7 +651,16 @@ namespace OpenMS p.setIntensity(pre_int_NH3_ * it->getIntensity()); if (add_metainfo_) { - String ion_name("[M+H]-NH3" + String((Size)charge, '+')); + String ion_name; + if (charge == 1) + { + ion_name = "[M+H-NH3]+"; + } + else + { + ion_name = "[M+" + String(charge) + "H-NH3]" + String(charge) + "+"; + } + ion_names.push_back(ion_name); charges.push_back(charge); } @@ -648,7 +673,15 @@ namespace OpenMS p.setIntensity(pre_int_NH3_); if (add_metainfo_) { - String ion_name("[M+H]-NH3" + String((Size)charge, '+')); + String ion_name; + if (charge == 1) + { + ion_name = "[M+H-NH3]+"; + } + else + { + ion_name = "[M+" + String(charge) + "H-NH3]" + String(charge) + "+"; + } ion_names.push_back(ion_name); charges.push_back(charge); } diff --git a/src/tests/topp/RNPxlSearch_1_output.idXML b/src/tests/topp/RNPxlSearch_1_output.idXML index 548c0b38284..012cb77b628 100644 --- a/src/tests/topp/RNPxlSearch_1_output.idXML +++ b/src/tests/topp/RNPxlSearch_1_output.idXML @@ -6,7 +6,7 @@ - + @@ -26,7 +26,7 @@ - + @@ -73,7 +73,7 @@ - + @@ -119,22 +119,22 @@ - + - + - - - + + + - + @@ -167,7 +167,7 @@ - + @@ -214,7 +214,7 @@ - + @@ -260,22 +260,22 @@ - - - + + + - - - + + + - + @@ -308,7 +308,7 @@ - + @@ -402,7 +402,7 @@ - + @@ -449,7 +449,7 @@ - + @@ -496,7 +496,7 @@ - + @@ -590,7 +590,7 @@ - + @@ -637,7 +637,7 @@ - + @@ -684,7 +684,7 @@ - + @@ -731,7 +731,7 @@ - + @@ -778,7 +778,7 @@ - + @@ -825,7 +825,7 @@ - + @@ -871,22 +871,22 @@ - + - + - - - + + + - + @@ -918,22 +918,22 @@ - + - + - - - + + + - + diff --git a/src/tests/topp/RNPxlSearch_2_output.idXML b/src/tests/topp/RNPxlSearch_2_output.idXML index 21561ef0893..b551b43e791 100644 --- a/src/tests/topp/RNPxlSearch_2_output.idXML +++ b/src/tests/topp/RNPxlSearch_2_output.idXML @@ -6,7 +6,7 @@ - + @@ -26,7 +26,7 @@ - + @@ -74,7 +74,7 @@ - + @@ -123,20 +123,20 @@ - + - - - + + + - + @@ -163,14 +163,14 @@ - + - + @@ -218,7 +218,7 @@ - + @@ -266,21 +266,21 @@ - - + + - - - + + + - + @@ -307,14 +307,14 @@ - + - + @@ -410,7 +410,7 @@ - + @@ -458,7 +458,7 @@ - + @@ -506,7 +506,7 @@ - + @@ -602,7 +602,7 @@ - + @@ -650,7 +650,7 @@ - + @@ -698,7 +698,7 @@ - + @@ -746,7 +746,7 @@ - + @@ -794,7 +794,7 @@ - + @@ -842,7 +842,7 @@ - + @@ -891,20 +891,20 @@ - + - - - + + + - + @@ -931,7 +931,7 @@ - + @@ -939,20 +939,20 @@ - + - - - + + + - + @@ -979,7 +979,7 @@ - + diff --git a/src/tests/topp/RNPxlSearch_3_output.idXML b/src/tests/topp/RNPxlSearch_3_output.idXML index 125044ce299..08c3a280b12 100644 --- a/src/tests/topp/RNPxlSearch_3_output.idXML +++ b/src/tests/topp/RNPxlSearch_3_output.idXML @@ -1,11 +1,12 @@ - + + - + @@ -24,27 +25,27 @@ - - - - - + + + + + - + - - - + + + - + - - + + @@ -67,22 +68,22 @@ - - - + + + - + - + - + - + @@ -114,22 +115,22 @@ - - - + + + - + - + - + - + - + @@ -161,22 +162,22 @@ - - - + + + - + - + - + - + - + @@ -208,28 +209,28 @@ - - - - - - - + + + + + + + - - - + + + - + - - - + + + @@ -255,27 +256,27 @@ - - - + + + - + - + - + - + - - + + @@ -298,22 +299,22 @@ - - - + + + - + - + - + - + @@ -345,22 +346,22 @@ - - - - - + + + + + - + - - - + + + - + @@ -388,22 +389,22 @@ - - - + + + - + - + - + @@ -435,22 +436,22 @@ - - - + + + - + - + - + - + - + @@ -482,27 +483,27 @@ - - - - - + + + + + - + - - - + + + - + - - + + @@ -525,22 +526,22 @@ - - - - - + + + + + - - - + + + - + @@ -572,27 +573,27 @@ - - - + + + - + - + - + - + - + - - + + @@ -619,22 +620,22 @@ - - - + + + - + - + - + - + - + @@ -666,27 +667,27 @@ - - - + + + - + - + - + - + - - + + @@ -713,22 +714,65 @@ - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + @@ -736,7 +780,7 @@ - + @@ -760,27 +804,27 @@ - - - - - + + + + + - - - + + + - + - - + + @@ -807,22 +851,22 @@ - - - + + + - + - + - + - + - + @@ -854,27 +898,27 @@ - - - - - - - + + + + + + + - - - + + + - + - - + + @@ -901,27 +945,27 @@ - - - + + + - + - + - + - + - + - - + + @@ -948,27 +992,27 @@ - - - + + + - - + + - + - + - + - - + + @@ -991,22 +1035,65 @@ - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + @@ -1014,7 +1101,7 @@ - + @@ -1038,27 +1125,27 @@ - - - + + + - + - + - + - + - + - - + + @@ -1085,27 +1172,27 @@ - - - - - + + + + + - + - - - + + + - + - - + + @@ -1132,22 +1219,22 @@ - - - + + + - + - + - - - + + + - + diff --git a/src/tests/topp/RNPxlSearch_3_output2.tsv b/src/tests/topp/RNPxlSearch_3_output2.tsv index 654b505cd9f..28ec5b91e1d 100644 --- a/src/tests/topp/RNPxlSearch_3_output2.tsv +++ b/src/tests/topp/RNPxlSearch_3_output2.tsv @@ -1,26 +1,28 @@ #RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.06231 A_330.06033 C_112.05108 C_306.0491 G_152.05723 G_346.05525 U_113.03509 U_307.03311 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank -17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 7.69674253463745 3.20641875267029 0 0 16.86 0 0 7.87 0 0 0 320.64 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 -17.788 712.7828 Cas6e UU-H2O1 LRANPIK 2 0.090044192969799 0 0 0 0 0 0 0 0 LRANPIK 810.5076 612.0506 1422.5582 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.4965 697.0 1423.5655 712.2864 475.1933 356.6468 2 -18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.68516635894775 2.21110057830811 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 -25.116 508.1855 Cas5 AU YTPYLGR 3 2.28572154045105 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 -26.237 678.2844 Cas5 U DYHTVLGAR 2 12.1896953582764 0.0519835986196995 0 5.20 0 0 0 0 0 0 0 DyHTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 -26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 18.437629699707 0.253752440214157 25.38 21.64 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 -26.413 791.8590 Cas5 CU-H2O1-H1O3P1 MRSYLILR 2 0.113123878836632 0 0 0 0 0 0 0 0 0 MRSYLILR 1050.6008 531.1003 1581.7011 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0012 1.5 1582.7084 791.8578 528.2410 396.4325 2 -28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.0651416778564 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 -28.487 828.6961 Cas5 CU-H2O1-H1O3P1 DDTSSLQALSESVQFAVR 3 1.20521605014801 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 DDTSSLQALSESVQFAVR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 -28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.97172045707703 0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 -31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.32002639770508 5.02087736129761 0 0 0 0 0 0 0 0 0 502.09 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 -31.812 957.3968 Cse2 GU-H2O1-H1O3P1 LVQPFGWENPR 2 0.699610769748688 0 0 0 0 0 0 0 0 0 0 0 0 LVQPFGWENPR 1341.6830 571.1064 1912.7894 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 0.0052 -5.4 1913.7967 957.4020 638.6037 479.2046 2 -33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74696397781372 3.93728351593018 0 0 393.73 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 -33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 9.35551738739014 0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 -34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7018890380859 3.19935750961304 319.94 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 -34.072 648.2559 Cas5 UU-H2O1 AVLKPR 2 0.141841292381287 0 0 0 0 0 0 0 AVLKPR 682.4490 612.0506 1294.4996 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0012 -1.8 1295.5069 648.2571 432.5071 324.6322 1 -36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 13.1162643432617 2.20912766456604 0 0 0 0 0 0 220.91 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 -36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 9.67764759063721 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 -37.098 735.8139 Cse1 U ALYTFAEGFK 2 13.8854703903198 1.3745938539505 16.33 0 0 0 105.82 118.19 0 137.46 0 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 -37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.48794269561768 4.0868239402771 0 0 0 0 0 0 408.68 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 -37.864 698.2974 Cas5 U DEPMITLPR 2 10.3223762512207 0.18551279604435 0 0 18.55 0 0 0 0 11.57 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 -37.864 698.2974 Cas7 CU-H2O1-H1O3P1 DAIFGGKR 2 0.214722290635109 0 0 0 0 0 0 0 0 0 DAIFGGKR 862.4661 531.1003 1393.5664 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.5069 726.4 1394.5736 697.7905 465.5294 349.3989 2 -39.118 623.2540 Cse2 U MLTWWGK 2 3.63084125518799 0.95687198638916 0 0 0 95.69 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 -39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 8.496826171875 1.10095739364624 0 0 0 0 0 0 0 0 110.10 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 -40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 4.66531610488892 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 +17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 9.6503963470459 3.3154616355896 0 0 16.86 0 0 7.87 0 0 0 331.55 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 +17.788 712.7828 Cas6e UU-H2O1 LRANPIK 2 0.090246170759201 0 0 0 0 0 0 0 0 LRANPIK 810.5076 612.0506 1422.5582 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.4965 697.0 1423.5655 712.2864 475.1933 356.6468 2 +18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.6882381439209 2.21110057830811 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 +25.116 508.1855 Cas5 AU YTPYLGR 3 2.29488754272461 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 +26.237 678.2844 Cas5 U DYHTVLGAR 2 12.8916025161743 0.669801533222198 0 5.20 66.98 0 38.44 0 0 0 0 DYhTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 +26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 18.4397106170654 0.31447559595108 31.45 27.71 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 +26.413 791.8590 Cas5 CU-H2O1-H1O3P1 MRSYLILR 2 0.113397143781185 0 0 0 0 0 0 0 0 0 MRSYLILR 1050.6008 531.1003 1581.7011 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0012 1.5 1582.7084 791.8578 528.2410 396.4325 2 +28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.0663547515869 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 +28.487 828.6961 Cas5 CU-H2O1-H1O3P1 DDTSSLQALSESVQFAVR 3 1.20592641830444 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 DDTSSLQALSESVQFAVR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 +28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.97541213035583 0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 +31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 11.8183317184448 4.78818416595459 0 0 0 0 0 21.64 0 0 0 478.82 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 +31.812 957.3968 Cse2 GU-H2O1-H1O3P1 LVQPFGWENPR 2 0.747869372367859 0 0 0 0 0 0 0 0 0 0 0 0 LVQPFGWENPR 1341.6830 571.1064 1912.7894 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 0.0052 -5.4 1913.7967 957.4020 638.6037 479.2046 2 +33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74868535995483 3.94590377807617 0 0 394.59 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 +33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 9.35625553131104 0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 +34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7075061798096 3.29842972755432 329.84 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 +34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 6.52631330490112 0.941199779510498 0 0 0 94.12 0 0 0 0 0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 +34.072 648.2559 Cas5 UU-H2O1 AVLKPR 2 0.14242060482502 0 0 0 0 0 0 0 AVLKPR 682.4490 612.0506 1294.4996 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0012 -1.8 1295.5069 648.2571 432.5071 324.6322 2 +36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 15.1146411895752 2.23655247688293 0 0 0 0 0 0 223.66 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 +36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 9.68333625793457 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 +37.098 735.8139 Cse1 U ALYTFAEGFK 2 15.285400390625 1.49806451797485 16.33 0 0 88.31 118.17 130.54 0 149.81 138.77 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 +37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.49998235702515 4.44108915328979 0 0 0 0 0 0 444.11 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 +37.864 698.2974 Cas5 U DEPMITLPR 2 10.3271074295044 0.301817148923874 0 0 30.18 0 0 0 0 17.27 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 +37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 0.245834589004517 0 0 0 0 0 0 0 0 GNIKRCR 845.4654 549.1108 1394.5762 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 +37.864 698.2974 Cas7 CU-H2O1-H1O3P1 DAIFGGKR 2 0.214921742677689 0 0 0 0 0 0 0 0 0 DAIFGGKR 862.4661 531.1003 1393.5664 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.5069 726.4 1394.5736 697.7905 465.5294 349.3989 3 +39.118 623.2540 Cse2 U MLTWWGK 2 3.63289213180542 1.09774243831635 0 0 0 109.77 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 +39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 9.60610485076904 1.2768223285675 0 0 0 0 0 0 0 0 127.68 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 +40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 4.67635536193848 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 diff --git a/src/tests/topp/RNPxlSearch_4_output.idXML b/src/tests/topp/RNPxlSearch_4_output.idXML index ddf7462a2a9..1ccf1553d3a 100644 --- a/src/tests/topp/RNPxlSearch_4_output.idXML +++ b/src/tests/topp/RNPxlSearch_4_output.idXML @@ -1,11 +1,12 @@ - + + - + @@ -37,26 +38,26 @@ - - - - + + + + - + - - - + + + - + - - + + @@ -78,29 +79,29 @@ - + - - - + + + - + - + - + - + - - + + @@ -122,28 +123,28 @@ - + - - - + + + - + - + - + - + - + @@ -170,28 +171,28 @@ - + - - - + + + - + - + - + - + - + @@ -218,34 +219,34 @@ - + - - - - - - + + + + + + - - - + + + - + - - - + + + @@ -266,24 +267,24 @@ - + - - - + + + - - + + - + - + - + @@ -310,33 +311,33 @@ - + - - + + - + - + - + - + - - + + @@ -358,36 +359,36 @@ - + - - - - - + + + + + - - - + + + - - + + - + - - + + - + - - + + @@ -396,34 +397,34 @@ - - - - - - - + + + + + + + - - - - + + + + - + - - - + + + - + @@ -450,29 +451,29 @@ - + - - - + + + - - - + + + - + - - + + @@ -494,28 +495,28 @@ - + - - + + - + - + - + - + - + @@ -542,33 +543,33 @@ - + - - - - + + + + - + - - - + + + - + - - + + @@ -590,24 +591,24 @@ - + - - - + + + - + - + - + - + - + @@ -634,33 +635,33 @@ - + - - - + + + - + - + - + - + - + - - + + @@ -682,29 +683,29 @@ - + - - - + + + - + - + - + - + - + - - + + @@ -726,28 +727,28 @@ - + - - + + - + - + - + - + - + @@ -774,33 +775,33 @@ - + - - + + - + - + - + - + - - + + @@ -822,28 +823,72 @@ - + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + @@ -851,7 +896,7 @@ - + @@ -870,33 +915,33 @@ - + - - - - + + + + - - - + + + - + - - + + @@ -918,24 +963,24 @@ - + - - - + + + - + - + - + - + @@ -962,28 +1007,28 @@ - + - - + + - + - + - + - + - + @@ -1010,24 +1055,24 @@ - + - - - + + + - + - + - + - + @@ -1054,33 +1099,33 @@ - + - - - - - - + + + + + + - - - + + + - + - - + + @@ -1102,24 +1147,24 @@ - + - - - + + + - - - + + + - + - + - + @@ -1146,33 +1191,33 @@ - + - - + + - + - + - + - + - + - - + + @@ -1194,33 +1239,33 @@ - + - - + + - - + + - + - + - + - - + + @@ -1242,36 +1287,36 @@ - + - - - + + + - + - + - + - + - - + + - + - - - + + + - - + + @@ -1280,39 +1325,39 @@ - - - - - - - + + + + + + + - - + + - + - + - + - + - + - - + + @@ -1334,33 +1379,33 @@ - + - - - - + + + + - + - - - + + + - + - - + + @@ -1382,24 +1427,24 @@ - + - - - + + + - + - + - + - + - + @@ -1426,28 +1471,28 @@ - + - - + + - + - + - - - + + + - + @@ -1474,7 +1519,7 @@ - + diff --git a/src/tests/topp/RNPxlSearch_4_output2.tsv b/src/tests/topp/RNPxlSearch_4_output2.tsv index bb9ab205aa6..317278a6a64 100644 --- a/src/tests/topp/RNPxlSearch_4_output2.tsv +++ b/src/tests/topp/RNPxlSearch_4_output2.tsv @@ -1,32 +1,33 @@ #RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.06231 A_330.06033 C_112.05108 C_306.0491 G_152.05723 G_346.05525 U_113.03509 U_307.03311 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank -17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 7.69674253463745 3.20641875267029 0 0 16.86 0 0 7.87 0 0 0 320.64 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 -17.788 712.7828 DECOY_Cas7 U-H2O1 KDDLNDAEAK 2 1.92921662330627 0.278845310211182 27.88 25.57 23.13 0 0 0 0 0 0 0 kDDLNDAEAK 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 2 -18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.68516635894775 2.21110057830811 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 -25.116 508.1855 Cas5 AU YTPYLGR 3 2.28572154045105 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 -26.237 678.2844 Cas5 U DYHTVLGAR 2 12.1896953582764 0.0519835986196995 0 5.20 0 0 0 0 0 0 0 DyHTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 -26.237 678.2844 DECOY_Cas5 U AGLVTHYDR 2 0.300964891910553 0.0519835986196995 0 0 0 0 0 0 5.20 0 0 AGLVTHyDR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 2 -26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 18.437629699707 0.253752440214157 25.38 21.64 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 -26.413 791.8590 Cas5 CU-H2O1-H1O3P1 MRSYLILR 2 0.113123878836632 0 0 0 0 0 0 0 0 0 MRSYLILR 1050.6008 531.1003 1581.7011 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0012 1.5 1582.7084 791.8578 528.2410 396.4325 2 -28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.0651416778564 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 -28.487 828.6961 DECOY_Cas5 CU-H2O1-H1O3P1 VAFQVSESLAQLSSTDDR 3 1.21061110496521 0.936702311038971 93.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 vAFQVSESLAQLSSTDDR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 -28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.97172045707703 0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 -31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.32002639770508 5.02087736129761 0 0 0 0 0 0 0 0 0 502.09 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 -31.812 957.3968 DECOY_Cse2 U IQACSGNDLQQWAR 2 1.43600630760193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 IQACSGNDLQQWAR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 2 -33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74696397781372 3.93728351593018 0 0 393.73 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 -33.237 510.2805 DECOY_Cas7 U-H2O1 LVKLLK 2 1.40568971633911 1.03232252597809 0 0 103.23 0 0 0 LVkLLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 -33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 9.35551738739014 0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 -34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7018890380859 3.19935750961304 319.94 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 -34.072 648.2559 Cas5 UU-H2O1 AVLKPR 2 0.141841292381287 0 0 0 0 0 0 0 AVLKPR 682.4490 612.0506 1294.4996 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0012 -1.8 1295.5069 648.2571 432.5071 324.6322 1 -36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 13.1162643432617 2.20912766456604 0 0 0 0 0 0 220.91 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 -36.528 938.3693 DECOY_Cse1 AU-H2O1 GNSPGGQPKLER 2 0.224538460373878 0 0 0 0 0 0 0 0 0 0 0 0 0 GNSPGGQPKLER 1238.6368 635.0778 1873.7146 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.5047 538.1 1874.7219 937.8646 625.5788 469.4359 2 -36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 9.67764759063721 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 -36.767 933.9406 DECOY_Cas7 U-H2O1 EAEDVSKGSLLALTK 2 0.208499565720558 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 EAEDVSKGSLLALTK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 2 -37.098 735.8139 Cse1 U ALYTFAEGFK 2 13.8854703903198 1.3745938539505 16.33 0 0 0 105.82 118.19 0 137.46 0 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 -37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 0.31612566113472 0 0 0 0 0 0 0 0 0 0 0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 -37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.48794269561768 4.0868239402771 0 0 0 0 0 0 408.68 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 -37.864 698.2974 Cas5 U DEPMITLPR 2 10.3223762512207 0.18551279604435 0 0 18.55 0 0 0 0 11.57 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 -37.864 698.2974 Cas7 CU-H2O1-H1O3P1 DAIFGGKR 2 0.214722290635109 0 0 0 0 0 0 0 0 0 DAIFGGKR 862.4661 531.1003 1393.5664 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.5069 726.4 1394.5736 697.7905 465.5294 349.3989 2 -39.118 623.2540 Cse2 U MLTWWGK 2 3.63084125518799 0.95687198638916 0 0 0 95.69 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 -39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 8.496826171875 1.10095739364624 0 0 0 0 0 0 0 0 110.10 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 -39.853 861.3889 DECOY_Cas5 U GTPRTGEFTPQGWAQMPGALR 3 2.99082112312317 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 GTPRTGEFTPQGWAQMPGALR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 2 -40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 4.66531610488892 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 +17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 9.6503963470459 3.3154616355896 0 0 16.86 0 0 7.87 0 0 0 331.55 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 +17.788 712.7828 DECOY_Cas7 U-H2O1 KDDLNDAEAK 2 1.92950487136841 0.277454644441605 27.75 25.43 22.99 0 0 0 0 0 0 0 kDDLNDAEAK 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 2 +18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.6882381439209 2.21110057830811 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 +25.116 508.1855 Cas5 AU YTPYLGR 3 2.29488754272461 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 +26.237 678.2844 Cas5 U DYHTVLGAR 2 12.8916025161743 0.669801533222198 0 5.20 66.98 0 38.44 0 0 0 0 DYhTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 +26.237 678.2844 DECOY_Cas5 U AGLVTHYDR 2 0.30169016122818 0.0519835986196995 0 0 0 0 0 0 5.20 0 0 AGLVTHyDR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 2 +26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 18.4397106170654 0.31447559595108 31.45 27.71 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 +26.413 791.8590 DECOY_Cas7 U-H2O1 QDFREGLKQR 2 0.862544894218445 0 0 0 0 0 0 0 0 0 0 0 QDFREGLKQR 1275.6684 306.0253 1581.6937 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0049 6.2 1582.7010 791.8541 528.2385 396.4307 2 +28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.0663547515869 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 +28.487 828.6961 DECOY_Cas5 CU-H2O1-H1O3P1 VAFQVSESLAQLSSTDDR 3 1.21134221553802 1.08878767490387 108.88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 vAFQVSESLAQLSSTDDR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 +28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.97541213035583 0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 +31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 11.8183317184448 4.78818416595459 0 0 0 0 0 21.64 0 0 0 478.82 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 +31.812 957.3968 DECOY_Cse2 U IQACSGNDLQQWAR 2 1.4375159740448 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 IQACSGNDLQQWAR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 2 +33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74868535995483 3.94590377807617 0 0 394.59 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 +33.237 510.2805 DECOY_Cas7 U-H2O1 LVKLLK 2 1.40665316581726 1.04094266891479 0 0 104.09 0 0 0 LVkLLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 +33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 9.35625553131104 0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 +34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7075061798096 3.29842972755432 329.84 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 +34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 6.52631330490112 0.941199779510498 0 0 0 94.12 0 0 0 0 0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 +34.072 648.2559 Cas5 UU-H2O1 AVLKPR 2 0.14242060482502 0 0 0 0 0 0 0 AVLKPR 682.4490 612.0506 1294.4996 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0012 -1.8 1295.5069 648.2571 432.5071 324.6322 2 +36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 15.1146411895752 2.23655247688293 0 0 0 0 0 0 223.66 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 +36.528 938.3693 DECOY_Cse1 AU-H2O1 GNSPGGQPKLER 2 0.225188031792641 0 0 0 0 0 0 0 0 0 0 0 0 0 GNSPGGQPKLER 1238.6368 635.0778 1873.7146 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.5047 538.1 1874.7219 937.8646 625.5788 469.4359 2 +36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 9.68333625793457 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 +36.767 933.9406 DECOY_Cas7 U-H2O1 EAEDVSKGSLLALTK 2 0.209372878074646 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 EAEDVSKGSLLALTK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 2 +37.098 735.8139 Cse1 U ALYTFAEGFK 2 15.285400390625 1.49806451797485 16.33 0 0 88.31 118.17 130.54 0 149.81 138.77 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 +37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 0.321959912776947 0 0 0 0 0 0 0 0 0 0 0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 +37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.49998235702515 4.44108915328979 0 0 0 0 0 0 444.11 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 +37.864 698.2974 Cas5 U DEPMITLPR 2 10.3271074295044 0.301817148923874 0 0 30.18 0 0 0 0 17.27 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 +37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 0.245834589004517 0 0 0 0 0 0 0 0 GNIKRCR 845.4654 549.1108 1394.5762 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 +39.118 623.2540 Cse2 U MLTWWGK 2 3.63289213180542 1.09774243831635 0 0 0 109.77 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 +39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 9.60610485076904 1.2768223285675 0 0 0 0 0 0 0 0 127.68 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 +39.853 861.3889 DECOY_Cas5 U GTPRTGEFTPQGWAQMPGALR 3 2.99445772171021 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 GTPRTGEFTPQGWAQMPGALR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 2 +40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 4.67635536193848 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index e65d2ac9a39..ea7f1fe8c4f 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -124,7 +124,7 @@ class RNPxlSearch : setValidFormats_("out_tsv", ListUtils::create("tsv")); registerTOPPSubsection_("precursor", "Precursor (Parent Ion) Options"); - registerDoubleOption_("precursor:mass_tolerance", "", 10.0, "Precursor mass tolerance (+/- around precursor m/z)", false); + registerDoubleOption_("precursor:mass_tolerance", "", 6.0, "Precursor mass tolerance (+/- around precursor m/z)", false); StringList precursor_mass_tolerance_unit_valid_strings; precursor_mass_tolerance_unit_valid_strings.emplace_back("ppm"); @@ -141,7 +141,7 @@ class RNPxlSearch : registerIntList_("precursor:isotopes", "", isotopes, "Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak)", false, false); registerTOPPSubsection_("fragment", "Fragments (Product Ion) Options"); - registerDoubleOption_("fragment:mass_tolerance", "", 10.0, "Fragment mass tolerance (+/- around fragment m/z)", false); + registerDoubleOption_("fragment:mass_tolerance", "", 20.0, "Fragment mass tolerance (+/- around fragment m/z)", false); StringList fragment_mass_tolerance_unit_valid_strings; fragment_mass_tolerance_unit_valid_strings.emplace_back("ppm"); @@ -155,14 +155,14 @@ class RNPxlSearch : ModificationsDB::getInstance()->getAllSearchModifications(all_mods); registerStringList_("modifications:fixed", "", ListUtils::create(""), "Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'", false); setValidStrings_("modifications:fixed", all_mods); - registerStringList_("modifications:variable", "", ListUtils::create(""), "Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'", false); + registerStringList_("modifications:variable", "", ListUtils::create("Oxidation (M)"), "Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'", false); setValidStrings_("modifications:variable", all_mods); registerIntOption_("modifications:variable_max_per_peptide", "", 2, "Maximum number of residues carrying a variable modification per candidate peptide", false, false); registerTOPPSubsection_("peptide", "Peptide Options"); registerIntOption_("peptide:min_size", "", 6, "Minimum size a peptide must have after digestion to be considered in the search.", false, true); registerIntOption_("peptide:max_size", "", 1e6, "Maximum size a peptide may have after digestion to be considered in the search.", false, true); - registerIntOption_("peptide:missed_cleavages", "", 1, "Number of missed cleavages.", false, false); + registerIntOption_("peptide:missed_cleavages", "", 2, "Number of missed cleavages.", false, false); StringList all_enzymes; ProteaseDB::getInstance()->getAllNames(all_enzymes); @@ -2074,8 +2074,8 @@ class RNPxlSearch : precursor_rna_weight, 2, // don't know the charge of the precursor at that point partial_loss_modification, - partial_loss_template_z1, - partial_loss_template_z2, + partial_loss_template_z1, + partial_loss_template_z2, partial_loss_template_z3, partial_loss_spectrum_z2); for (auto& n : partial_loss_spectrum_z2.getStringDataArrays()[0]) { n[0] = 'y'; } // hyperscore hack @@ -2412,10 +2412,12 @@ class RNPxlSearch : immonium_sub_score = 0; precursor_sub_score = 0; a_ion_sub_score = 0; - auto const & tl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - total_loss_spectrum); + auto const & tl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + total_loss_spectrum, + total_loss_spectrum.getIntegerDataArrays()[0]); tlss_MIC = tl_sub_scores.TIC != 0 ? tl_sub_scores.MIC / tl_sub_scores.TIC : 0; tlss_err = tl_sub_scores.err; @@ -2423,26 +2425,32 @@ class RNPxlSearch : if (!immonium_sub_score_spectrum.empty()) { - auto const & r = MorpheusScore::compute(fragment_mass_tolerance, + auto const & r = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - immonium_sub_score_spectrum); + exp_spectrum.getIntegerDataArrays()[0], + immonium_sub_score_spectrum, + immonium_sub_score_spectrum.getIntegerDataArrays()[0]); immonium_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } if (!precursor_sub_score_spectrum.empty()) { - auto const & r = MorpheusScore::compute(fragment_mass_tolerance, + auto const & r = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - precursor_sub_score_spectrum); + exp_spectrum.getIntegerDataArrays()[0], + precursor_sub_score_spectrum, + precursor_sub_score_spectrum.getIntegerDataArrays()[0]); precursor_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } if (!a_ion_sub_score_spectrum.empty()) { - auto const & r = MorpheusScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - a_ion_sub_score_spectrum); + auto const & r = MorpheusScore::compute(fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + a_ion_sub_score_spectrum, + a_ion_sub_score_spectrum.getIntegerDataArrays()[0]); a_ion_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } } @@ -2469,7 +2477,9 @@ class RNPxlSearch : auto const & r = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - marker_ions_sub_score_spectrum_z1); + exp_spectrum.getIntegerDataArrays()[0], + marker_ions_sub_score_spectrum_z1, + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0]); marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } //TODO: these are currently empty @@ -2493,7 +2503,9 @@ class RNPxlSearch : auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - partial_loss_spectrum_z1); + exp_spectrum.getIntegerDataArrays()[0], + partial_loss_spectrum_z1, + partial_loss_spectrum_z1.getIntegerDataArrays()[0]); plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; plss_err = pl_sub_scores.err; @@ -2510,7 +2522,9 @@ class RNPxlSearch : auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - partial_loss_spectrum_z2); + exp_spectrum.getIntegerDataArrays()[0], + partial_loss_spectrum_z2, + partial_loss_spectrum_z2.getIntegerDataArrays()[0]); plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; plss_err = pl_sub_scores.err; @@ -3079,7 +3093,6 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const S } } else // don't consider fragment ions with charge >= 4 - { break; } @@ -3123,7 +3136,15 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( / static_cast(charge); partial_loss_spectrum.push_back(Peak1D(xl_mz, 1.0)); partial_loss_spectrum_charge.push_back(charge); - partial_loss_spectrum_annotation.push_back(String("[M+") + precursor_rna_adduct + "]"); + if (charge > 1) + { + partial_loss_spectrum_annotation.push_back(String("[M+") + + String(charge) + "H+" + precursor_rna_adduct + "]"); + } + else + { + partial_loss_spectrum_annotation.push_back(String("[M+H+") + precursor_rna_adduct + "]"); + } } int main(int argc, const char** argv) From 7cdf7b9acf7e613484fbe559d35d325f7e9c7b6b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 8 Feb 2019 09:39:04 +0100 Subject: [PATCH 005/471] [FEATURE] added extra debug output to percolator --- src/topp/PercolatorAdapter.cpp | 46 ++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/src/topp/PercolatorAdapter.cpp b/src/topp/PercolatorAdapter.cpp index 5920399d174..fa0cb878b32 100644 --- a/src/topp/PercolatorAdapter.cpp +++ b/src/topp/PercolatorAdapter.cpp @@ -45,6 +45,8 @@ #include #include +#include + #include #include #include @@ -226,6 +228,15 @@ class PercolatorAdapter : registerOutputFile_("out_pin", "", "", "Write pin file (e.g., for debugging)", !is_required, is_advanced_option); setValidFormats_("out_pin", ListUtils::create("tab"), !force_openms_format); + registerOutputFile_("out_pout_target", "", "", "Write pout file (e.g., for debugging)", !is_required, is_advanced_option); + setValidFormats_("out_pout_target", ListUtils::create("tab"), !force_openms_format); + registerOutputFile_("out_pout_decoy", "", "", "Write pout file (e.g., for debugging)", !is_required, is_advanced_option); + setValidFormats_("out_pout_decoy", ListUtils::create("tab"), !force_openms_format); + registerOutputFile_("out_pout_target_proteins", "", "", "Write pout file (e.g., for debugging)", !is_required, is_advanced_option); + setValidFormats_("out_pout_target_proteins", ListUtils::create("tab"), !force_openms_format); + registerOutputFile_("out_pout_decoy_proteins", "", "", "Write pout file (e.g., for debugging)", !is_required, is_advanced_option); + setValidFormats_("out_pout_decoy_proteins", ListUtils::create("tab"), !force_openms_format); + registerStringOption_("out_type", "", "", "Output file type -- default: determined from file extension or content.", false); setValidStrings_("out_type", ListUtils::create("mzid,idXML,osw")); String enzs = "no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin"; @@ -1011,15 +1022,40 @@ class PercolatorAdapter : // when percolator finished calculation, it stores the results -r option (with or without -U) or -m (which seems to be not working) // WARNING: The -r option cannot be used in conjunction with -U: no peptide level statistics are calculated, redirecting PSM level statistics to provided file instead. map pep_map; + String pout_target = getStringOption_("out_pout_target"); + String pout_decoy = getStringOption_("out_pout_decoy"); + String pout_target_proteins = getStringOption_("out_pout_target_proteins"); + String pout_decoy_proteins = getStringOption_("out_pout_decoy_proteins"); + if (peptide_level_fdrs) { readPoutAsMap_(pout_target_file_peptides, pep_map); readPoutAsMap_(pout_decoy_file_peptides, pep_map); + + // copy file in tmp folder to output + if (!pout_target.empty()) + { + QFile::copy(pout_target_file_peptides.toQString(), pout_target.toQString()); + } + if (!pout_decoy.empty()) + { + QFile::copy(pout_decoy_file_peptides.toQString(), pout_decoy.toQString()); + } } else { readPoutAsMap_(pout_target_file, pep_map); readPoutAsMap_(pout_decoy_file, pep_map); + + // copy file in tmp folder to output + if (!pout_target.empty()) + { + QFile::copy(pout_target_file.toQString(), pout_target.toQString()); + } + if (!pout_decoy.empty()) + { + QFile::copy(pout_decoy_file.toQString(), pout_decoy.toQString()); + } } map protein_map; @@ -1027,6 +1063,16 @@ class PercolatorAdapter : { readProteinPoutAsMap_(pout_target_file_proteins, protein_map); readProteinPoutAsMap_(pout_decoy_file_proteins, protein_map); + + // copy file in tmp folder to output filename + if (!pout_target_proteins.empty()) + { + QFile::copy(pout_target_file_proteins.toQString(), pout_target_proteins.toQString()); + } + if (!pout_decoy_proteins.empty()) + { + QFile::copy(pout_target_file_proteins.toQString(), pout_decoy_proteins.toQString()); + } } // idXML or mzid input From e04a5c388b5eb215ec2461bad86da7d344abe7ca Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 8 Feb 2019 09:39:42 +0100 Subject: [PATCH 006/471] [FEATURE] add match odds score --- src/utils/RNPxlSearch.cpp | 189 +++++++++++++++++++++++++------------- 1 file changed, 125 insertions(+), 64 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index ea7f1fe8c4f..cbd802d2550 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -75,6 +75,7 @@ #include #include +#include #include #include @@ -169,7 +170,6 @@ class RNPxlSearch : registerStringOption_("peptide:enzyme", "", "Trypsin", "The enzyme used for peptide digestion.", false); setValidStrings_("peptide:enzyme", all_enzymes); - registerTOPPSubsection_("report", "Reporting Options"); registerIntOption_("report:top_hits", "", 1, "Maximum number of top scoring hits per spectrum that are reported.", false, true); @@ -341,10 +341,13 @@ class RNPxlSearch : float err = 0; float Morph = 0; + float modds = 0; // match odds + // partial loss morpheus related subscores float pl_MIC = 0; float pl_err = 0; float pl_Morph = 0; + float pl_modds = 0; // match odds // complete TIC fraction of explained peaks float total_MIC = 0; @@ -496,8 +499,6 @@ class RNPxlSearch : } } - - // prefix used to denote marker ions in fragment annotations static constexpr const char* ANNOTATIONS_MARKER_ION_PREFIX = "MI:"; @@ -1376,9 +1377,11 @@ class RNPxlSearch : ph.setMetaValue(String("RNPxl:MIC"), ah.MIC); ph.setMetaValue(String("RNPxl:err"), ah.err); ph.setMetaValue(String("RNPxl:Morph"), ah.Morph); + ph.setMetaValue(String("RNPxl:modds"), ah.modds); ph.setMetaValue(String("RNPxl:pl_MIC"), ah.pl_MIC); ph.setMetaValue(String("RNPxl:pl_err"), ah.pl_err); ph.setMetaValue(String("RNPxl:pl_Morph"), ah.pl_Morph); + ph.setMetaValue(String("RNPxl:pl_modds"), ah.pl_modds); ph.setMetaValue(String("RNPxl:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses ph.setMetaValue(String("RNPxl:RNA"), *mod_combinations_it->second.begin()); // return first nucleotide formula matching the index of the empirical formula @@ -1441,6 +1444,7 @@ class RNPxlSearch : << "isotope_error" << "RNPxl:score" << "RNPxl:total_loss_score" + << "RNPxl:modds" << "RNPxl:immonium_score" << "RNPxl:precursor_score" << "RNPxl:a_ion_score" @@ -1452,6 +1456,7 @@ class RNPxlSearch : << "RNPxl:pl_MIC" << "RNPxl:pl_err" << "RNPxl:pl_Morph" + << "RNPxl:pl_modds" << "RNPxl:total_MIC" << "RNPxl:RNA_MASS_z0"; if (!purities.empty()) feature_set << "precursor_purity"; @@ -1507,7 +1512,6 @@ class RNPxlSearch : } } - if (precursor_mass < small_peptide_mass_filter_threshold) { small_peptide_mass_filtered++; @@ -1962,7 +1966,8 @@ class RNPxlSearch : a_ion_sub_score(0), tlss_MIC(0), tlss_err(0), - tlss_Morph(0); + tlss_Morph(0), + tlss_modds(0); scoreTotalLossFragments_(exp_spectrum, total_loss_spectrum, @@ -1975,11 +1980,11 @@ class RNPxlSearch : tlss_MIC, tlss_err, tlss_Morph, + tlss_modds, immonium_sub_score, precursor_sub_score, a_ion_sub_score); - // bad score, likely wihout any single matching peak if (total_loss_score < 0.01) { continue; } @@ -1990,6 +1995,7 @@ class RNPxlSearch : ah.MIC = tlss_MIC; ah.err = tlss_err; ah.Morph = tlss_Morph; + ah.modds = tlss_modds; ah.total_loss_score = total_loss_score; ah.immonium_score = immonium_sub_score; ah.precursor_score = precursor_sub_score; @@ -2096,10 +2102,20 @@ class RNPxlSearch : const Size& scan_index = l->second.first; const int& isotope_error = l->second.second; const PeakSpectrum& exp_spectrum = spectra[scan_index]; - float tlss_MIC(0), tlss_err(0), tlss_Morph(0), - immonium_sub_score(0), precursor_sub_score(0), - a_ion_sub_score(0), partial_loss_sub_score(0), marker_ions_sub_score(0), - plss_MIC(0), plss_err(0), plss_Morph(0), score; + float tlss_MIC(0), + tlss_err(1.0), + tlss_Morph(0), + tlss_modds(0), + immonium_sub_score(0), + precursor_sub_score(0), + a_ion_sub_score(0), + partial_loss_sub_score(0), + marker_ions_sub_score(0), + plss_MIC(0), + plss_err(1.0), + plss_Morph(0), + plss_modds(0), + score(0); const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); PeakSpectrum & total_loss_spectrum = (exp_pc_charge < 3) ? total_loss_spectrum_z1 : total_loss_spectrum_z2; @@ -2114,6 +2130,7 @@ class RNPxlSearch : tlss_MIC, tlss_err, tlss_Morph, + tlss_modds, immonium_sub_score, precursor_sub_score, a_ion_sub_score); @@ -2122,12 +2139,17 @@ class RNPxlSearch : if (score < 0.01) { continue; } scorePartialLossFragments_(exp_spectrum, - fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - partial_loss_spectrum_z1, partial_loss_spectrum_z2, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + partial_loss_spectrum_z1, + partial_loss_spectrum_z2, marker_ions_sub_score_spectrum_z1, partial_loss_sub_score, marker_ions_sub_score, - plss_MIC, plss_err, plss_Morph); + plss_MIC, + plss_err, + plss_Morph, + plss_modds); // add peptide hit AnnotatedHit ah; @@ -2137,9 +2159,11 @@ class RNPxlSearch : ah.MIC = tlss_MIC; ah.err = tlss_err; ah.Morph = tlss_Morph; + ah.modds = tlss_modds; ah.pl_MIC = plss_MIC; ah.pl_err = plss_err; ah.pl_Morph = plss_Morph; + ah.pl_modds = plss_modds; ah.immonium_score = immonium_sub_score; ah.precursor_score = precursor_sub_score; ah.a_ion_score = a_ion_sub_score; @@ -2188,13 +2212,14 @@ class RNPxlSearch : const Size &scan_index = l->second.first; const int &isotope_error = l->second.second; const PeakSpectrum &exp_spectrum = spectra[scan_index]; - float total_loss_score; - float immonium_sub_score; - float precursor_sub_score; - float a_ion_sub_score; - float tlss_MIC; - float tlss_err; - float tlss_Morph; + float total_loss_score(0), + immonium_sub_score(0), + precursor_sub_score(0), + a_ion_sub_score(0), + tlss_MIC(0), + tlss_err(1.0), + tlss_Morph(0), + tlss_modds(0); const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); PeakSpectrum & total_loss_spectrum = (exp_pc_charge < 3) ? total_loss_spectrum_z1 : total_loss_spectrum_z2; @@ -2210,6 +2235,7 @@ class RNPxlSearch : tlss_MIC, tlss_err, tlss_Morph, + tlss_modds, immonium_sub_score, precursor_sub_score, a_ion_sub_score); @@ -2225,6 +2251,7 @@ class RNPxlSearch : ah.MIC = tlss_MIC; ah.err = tlss_err; ah.Morph = tlss_Morph; + ah.modds = tlss_modds; ah.immonium_score = immonium_sub_score; ah.precursor_score = precursor_sub_score; ah.a_ion_score = a_ion_sub_score; @@ -2307,18 +2334,24 @@ class RNPxlSearch : postScoreHits_(spectra, annotated_hits, report_top_hits, - mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, + mm, + fixed_modifications, + variable_modifications, + max_variable_mods_per_peptide, partial_loss_spectrum_generator, - fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, all_feasible_fragment_adducts); progresslogger.startProgress(0, 1, "Post-processing and annotation..."); postProcessHits_(spectra, annotated_hits, - protein_ids, peptide_ids, + protein_ids, + peptide_ids, report_top_hits, mm, - fixed_modifications, variable_modifications, + fixed_modifications, + variable_modifications, max_variable_mods_per_peptide, purities); progresslogger.endProgress(); @@ -2383,6 +2416,45 @@ class RNPxlSearch : return EXECUTION_OK; } + static double matchOddsScore_( + const PeakSpectrum& theoretical_spec, + const Size matched_size, + const double fragment_mass_tolerance, + const bool fragment_mass_tolerance_unit_ppm) + { + using boost::math::binomial; + Size theo_size = theoretical_spec.size(); + + if (matched_size < 1 || theo_size < 1) { return 0; } + + double range = theoretical_spec[theo_size-1].getMZ() - theoretical_spec[0].getMZ(); + + // Compute fragment tolerance in Da for the mean of MZ values, if tolerance in ppm (rough approximation) + double mean = 0.0; + for (Size i = 0; i < theo_size; ++i) { mean += theoretical_spec[i].getMZ(); } + mean /= (double)theo_size; + double tolerance_Th = fragment_mass_tolerance_unit_ppm ? mean * 1e-6 * fragment_mass_tolerance : fragment_mass_tolerance; + + // A priori probability of a random match given info about the theoretical spectrum + double a_priori_p = (1 - ( pow( (1 - 2 * tolerance_Th / (0.5 * range)), static_cast(theo_size)))); + + double match_odds = 0; + + binomial flip(theo_size, a_priori_p); + // min double number to avoid 0 values, causing scores with the value "inf" + match_odds = -log(1 - cdf(flip, matched_size) + std::numeric_limits::min()); + + // score lower than 0 does not make sense, but can happen if cfd = 0, -log( 1 + min() ) < 0 + if (match_odds >= 0.0) + { + return match_odds; + } + else + { + return 0; + } + } + // determine main score and sub scores of peaks without shifts void scoreTotalLossFragments_(const PeakSpectrum &exp_spectrum, const PeakSpectrum &total_loss_spectrum, @@ -2395,6 +2467,7 @@ class RNPxlSearch : float &tlss_MIC, float &tlss_err, float &tlss_Morph, + float &tlss_modds, float &immonium_sub_score, float &precursor_sub_score, float &a_ion_sub_score) const @@ -2422,6 +2495,10 @@ class RNPxlSearch : tlss_MIC = tl_sub_scores.TIC != 0 ? tl_sub_scores.MIC / tl_sub_scores.TIC : 0; tlss_err = tl_sub_scores.err; tlss_Morph = tl_sub_scores.score; + tlss_modds = matchOddsScore_(total_loss_spectrum, + (int)tlss_Morph, // = number of matched peaks + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm); if (!immonium_sub_score_spectrum.empty()) { @@ -2463,7 +2540,10 @@ class RNPxlSearch : const PeakSpectrum &marker_ions_sub_score_spectrum_z1, float &partial_loss_sub_score, float &marker_ions_sub_score, - float &plss_MIC, float &plss_err, float &plss_Morph) const + float &plss_MIC, + float &plss_err, + float &plss_Morph, + float &plss_modds) const { const SignedSize& exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); @@ -2471,7 +2551,6 @@ class RNPxlSearch : plss_err = 0; plss_Morph = 0; - if (!marker_ions_sub_score_spectrum_z1.empty()) { auto const & r = MorpheusScore::compute(fragment_mass_tolerance, @@ -2492,53 +2571,35 @@ class RNPxlSearch : */ if (!partial_loss_spectrum_z1.empty()) // check if we generated partial loss spectra { - if (exp_pc_charge < 3) + MSSpectrum const * pl_spec = &partial_loss_spectrum_z1; + if (exp_pc_charge >= 3) { - partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - partial_loss_spectrum_z1, - partial_loss_spectrum_z1.getIntegerDataArrays()[0]); - auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - partial_loss_spectrum_z1, - partial_loss_spectrum_z1.getIntegerDataArrays()[0]); - - plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; - plss_err = pl_sub_scores.err; - plss_Morph = pl_sub_scores.score; - } - else //if (exp_pc_charge >= 3) - { - partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - partial_loss_spectrum_z2, - partial_loss_spectrum_z2.getIntegerDataArrays()[0]); - auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - partial_loss_spectrum_z2, - partial_loss_spectrum_z2.getIntegerDataArrays()[0]); - - plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; - plss_err = pl_sub_scores.err; - plss_Morph = pl_sub_scores.score; + pl_spec = &partial_loss_spectrum_z2; } + partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + *pl_spec, + pl_spec->getIntegerDataArrays()[0]); + auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + *pl_spec, + pl_spec->getIntegerDataArrays()[0]); + plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; + plss_err = pl_sub_scores.err; + plss_Morph = pl_sub_scores.score; + plss_modds = matchOddsScore_(*pl_spec, (int)plss_Morph, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm); } #ifdef DEBUG_RNPXLSEARCH LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif - // TODO: cap plss_err + // cap plss_err float ft_da = fragment_mass_tolerance_unit_ppm ? fragment_mass_tolerance * 1e-6 * 1000.0 : fragment_mass_tolerance; if (plss_err > ft_da) plss_err = ft_da; } - }; vector RNPxlSearch::RNPxlParameterParsing::getModifications(StringList modNames) { From 4dc1ab4a08754387c573014756ba75353428c9b8 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 8 Feb 2019 10:24:14 +0100 Subject: [PATCH 007/471] [FEATURE] export precursor itensity for percolator --- src/utils/RNPxlSearch.cpp | 39 ++++++++++++++++++++++++--------------- 1 file changed, 24 insertions(+), 15 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index cbd802d2550..fe198c918d2 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -1327,17 +1327,20 @@ class RNPxlSearch : #endif for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) { + const MSSpectrum& spec = exp[scan_index]; if (!annotated_hits[scan_index].empty()) { // create empty PeptideIdentification object and fill meta data PeptideIdentification pi; pi.setMetaValue("scan_index", static_cast(scan_index)); + pi.setMetaValue("spectrum_reference", spec.getNativeID()); pi.setScoreType("hyperscore"); pi.setHigherScoreBetter(true); - pi.setRT(exp[scan_index].getRT()); - pi.setMZ(exp[scan_index].getPrecursors()[0].getMZ()); - pi.setMetaValue("precursor_intensity", exp[scan_index].getPrecursors()[0].getIntensity()); - Size charge = exp[scan_index].getPrecursors()[0].getCharge(); + pi.setRT(spec.getRT()); + pi.setMZ(spec.getPrecursors()[0].getMZ()); + double precursor_intensity_log10 = log10(1.0 + spec.getPrecursors()[0].getIntensity()); + pi.setMetaValue("precursor_intensity_log10", precursor_intensity_log10); + Size charge = spec.getPrecursors()[0].getCharge(); // create full peptide hit structure from annotated hits vector phs; @@ -1392,6 +1395,9 @@ class RNPxlSearch : ph.setMetaValue(String("RNPxl:localization_scores"), ah.localization_scores); ph.setMetaValue(String("RNPxl:best_localization"), ah.best_localization); + // also annotate PI to hit so it is available to percolator + ph.setMetaValue("precursor_intensity_log10", precursor_intensity_log10); + if (!purities.empty()) { ph.setMetaValue("precursor_purity", purities[scan_index].signal_proportion); @@ -1458,7 +1464,8 @@ class RNPxlSearch : << "RNPxl:pl_Morph" << "RNPxl:pl_modds" << "RNPxl:total_MIC" - << "RNPxl:RNA_MASS_z0"; + << "RNPxl:RNA_MASS_z0" + << "precursor_intensity_log10"; if (!purities.empty()) feature_set << "precursor_purity"; search_parameters.setMetaValue("feature_extractor", "TOPP_PSMFeatureExtractor"); @@ -2436,18 +2443,18 @@ class RNPxlSearch : double tolerance_Th = fragment_mass_tolerance_unit_ppm ? mean * 1e-6 * fragment_mass_tolerance : fragment_mass_tolerance; // A priori probability of a random match given info about the theoretical spectrum - double a_priori_p = (1 - ( pow( (1 - 2 * tolerance_Th / (0.5 * range)), static_cast(theo_size)))); + long double a_priori_p = (1 - ( pow( (1 - 2 * tolerance_Th / (0.5 * range)), static_cast(theo_size)))); - double match_odds = 0; + long double match_odds(0); binomial flip(theo_size, a_priori_p); // min double number to avoid 0 values, causing scores with the value "inf" - match_odds = -log(1 - cdf(flip, matched_size) + std::numeric_limits::min()); + match_odds = -log(1 - cdf(flip, (long double)matched_size) + std::numeric_limits::min()); // score lower than 0 does not make sense, but can happen if cfd = 0, -log( 1 + min() ) < 0 if (match_odds >= 0.0) { - return match_odds; + return (double)match_odds; } else { @@ -2480,7 +2487,13 @@ class RNPxlSearch : total_loss_spectrum.getIntegerDataArrays()[0]); // bad score, likely wihout any single matching peak - if (total_loss_score < 0.01) { return; } + if (total_loss_score < 0.01) + { + // cap total loss error to a large value + float ft_da = fragment_mass_tolerance_unit_ppm ? fragment_mass_tolerance * 1e-6 * 1000.0 : fragment_mass_tolerance; + if (tlss_err > ft_da) tlss_err = ft_da; + return; + } immonium_sub_score = 0; precursor_sub_score = 0; @@ -2547,10 +2560,6 @@ class RNPxlSearch : { const SignedSize& exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); - plss_MIC = 0; - plss_err = 0; - plss_Morph = 0; - if (!marker_ions_sub_score_spectrum_z1.empty()) { auto const & r = MorpheusScore::compute(fragment_mass_tolerance, @@ -2596,7 +2605,7 @@ class RNPxlSearch : #ifdef DEBUG_RNPXLSEARCH LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif - // cap plss_err + // cap plss_err to something larger than the mean_mz * max_ppm_error float ft_da = fragment_mass_tolerance_unit_ppm ? fragment_mass_tolerance * 1e-6 * 1000.0 : fragment_mass_tolerance; if (plss_err > ft_da) plss_err = ft_da; } From a91932438d55335c3afc282342138758719503aa Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 8 Feb 2019 14:25:00 +0100 Subject: [PATCH 008/471] [TEST] add slow scoring test --- src/tests/topp/CMakeLists.txt | 6 + src/tests/topp/RNPxlSearch_5_output.idXML | 1048 +++++++++++++++++++++ 2 files changed, 1054 insertions(+) create mode 100644 src/tests/topp/RNPxlSearch_5_output.idXML diff --git a/src/tests/topp/CMakeLists.txt b/src/tests/topp/CMakeLists.txt index 6752d814323..d2673349109 100644 --- a/src/tests/topp/CMakeLists.txt +++ b/src/tests/topp/CMakeLists.txt @@ -1687,6 +1687,12 @@ add_test("TOPP_RNPxlSearch_4_out2" ${DIFF} -in1 RNPxlSearch_4_output2.tmp -in2 $ set_tests_properties("TOPP_RNPxlSearch_4_out1" PROPERTIES DEPENDS "TOPP_RNPxlSearch_4") set_tests_properties("TOPP_RNPxlSearch_4_out2" PROPERTIES DEPENDS "TOPP_RNPxlSearch_4") +# test internal decoy generation - slow scoring +add_test("TOPP_RNPxlSearch_5" ${TOPP_BIN_PATH}/RNPxlSearch -test -in +${DATA_DIR_TOPP}/RNPxlSearch_1_input.mzML -database ${DATA_DIR_TOPP}/RNPxlSearch_1_input.fasta -out RNPxlSearch_5_output.tmp -RNPxl:decoys -ini ${DATA_DIR_TOPP}/RNPxlSearch_1_parameters.ini -RNPxl:scoring slow) +add_test("TOPP_RNPxlSearch_5_out1" ${DIFF} -whitelist "IdentificationRun date" +"db=" -in1 RNPxlSearch_5_output.tmp -in2 ${DATA_DIR_TOPP}/RNPxlSearch_5_output.idXML ) +set_tests_properties("TOPP_RNPxlSearch_5_out1" PROPERTIES DEPENDS "TOPP_RNPxlSearch_5") #------------------------------------------------------------------------------ # RTModel tests add_test("TOPP_RTModel_1" ${TOPP_BIN_PATH}/RTModel -test -in ${DATA_DIR_TOPP}/RTModel_1_input.idXML -out RTModel_1_output.tmp -ini ${DATA_DIR_TOPP}/RTModel_1_parameters.ini) diff --git a/src/tests/topp/RNPxlSearch_5_output.idXML b/src/tests/topp/RNPxlSearch_5_output.idXML new file mode 100644 index 00000000000..494fd2d3e6f --- /dev/null +++ b/src/tests/topp/RNPxlSearch_5_output.idXML @@ -0,0 +1,1048 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 2dd9d6db7466a48493ec92f6a37273d39ad05bee Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 12 Feb 2019 18:38:35 +0100 Subject: [PATCH 009/471] [FIX] moved spectrum generation out of loop --- src/utils/RNPxlSearch.cpp | 35 +++++++++++++++++++++++------------ 1 file changed, 23 insertions(+), 12 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 51d2267cbe5..a437b295dfa 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -703,6 +703,8 @@ class RNPxlSearch : new_param.setValue("add_all_precursor_charges", "true"); new_param.setValue("add_abundant_immonium_ions", "true"); new_param.setValue("add_losses", "true"); + new_param.setValue("add_a_ions", "true"); + tmp_generator.setParameters(new_param); tmp_generator.getSpectrum(total_loss_spectrum, fixed_and_variable_modified_peptide, 1, precursor_charge); @@ -714,7 +716,10 @@ class RNPxlSearch : total_loss_spectrum.getStringDataArrays()[0]); total_loss_spectrum.sortByPosition(); // need to resort after adding special immonium ions - PeakSpectrum partial_loss_spectrum, partial_loss_template_z1, partial_loss_template_z2, partial_loss_template_z3; + PeakSpectrum partial_loss_spectrum, + partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3; partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); @@ -1450,13 +1455,13 @@ class RNPxlSearch : */ StringList feature_set; feature_set -// << "isotope_error" -// << "RNPxl:score" + << "isotope_error" + << "RNPxl:score" << "RNPxl:total_loss_score" << "RNPxl:modds" << "RNPxl:immonium_score" << "RNPxl:precursor_score" -// << "RNPxl:a_ion_score" + << "RNPxl:a_ion_score" << "RNPxl:marker_ions_score" << "RNPxl:partial_loss_score" << "RNPxl:MIC" @@ -1467,7 +1472,7 @@ class RNPxlSearch : << "RNPxl:pl_Morph" << "RNPxl:pl_modds" << "RNPxl:total_MIC" -// << "RNPxl:RNA_MASS_z0" + << "RNPxl:RNA_MASS_z0" << "precursor_intensity_log10"; if (!purities.empty()) feature_set << "precursor_purity"; @@ -1912,7 +1917,9 @@ class RNPxlSearch : Size rna_mod_index = 0; // TODO: track the XL-able nt here - for (std::map::const_iterator rna_mod_it = mm.mod_masses.begin(); rna_mod_it != mm.mod_masses.end(); ++rna_mod_it, ++rna_mod_index) + for (std::map::const_iterator rna_mod_it = mm.mod_masses.begin(); + rna_mod_it != mm.mod_masses.end(); + ++rna_mod_it, ++rna_mod_index) { const double precursor_rna_weight = rna_mod_it->second; const double current_peptide_mass = current_peptide_mass_without_RNA + precursor_rna_weight; // add RNA mass @@ -1958,10 +1965,6 @@ class RNPxlSearch : if (!fast_scoring_) { - PeakSpectrum marker_ions_sub_score_spectrum_z1; - //shifted_immonium_ions_sub_score_spectrum; - PeakSpectrum partial_loss_spectrum_z1, partial_loss_spectrum_z2; - // retrieve RNA adduct name auto mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, rna_mod_index); @@ -2071,12 +2074,19 @@ class RNPxlSearch : // Do we have (nucleotide) specific fragmentation adducts? for the current RNA adduct on the precursor? // If so, generate spectra for shifted ion series + // score individually for every nucleotide for (auto const & nuc_2_adducts : feasible_MS2_adducts) { + // determine current nucleotide and associated partial losses const char& cross_linked_nucleotide = nuc_2_adducts.first; const vector& partial_loss_modification = nuc_2_adducts.second; + PeakSpectrum marker_ions_sub_score_spectrum_z1, + partial_loss_spectrum_z1, + partial_loss_spectrum_z2; + + // nucleotide is associated with certain NA-related fragment losses? if (!partial_loss_modification.empty()) { // shifted b- / y- / a-ions @@ -2087,8 +2097,8 @@ class RNPxlSearch : precursor_rna_weight, 1, partial_loss_modification, - partial_loss_template_z1, - partial_loss_template_z2, + partial_loss_template_z1, + partial_loss_template_z2, partial_loss_template_z3, partial_loss_spectrum_z1); for (auto& n : partial_loss_spectrum_z1.getStringDataArrays()[0]) { n[0] = 'y'; } // hyperscore hack @@ -2449,6 +2459,7 @@ class RNPxlSearch : // compute p score as e.g. in the AScore implementation or Andromeda const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see ThresholdMower) const double pscore = -10.0 * log10(a_score_algorithm.computeCumulativeScore(N, matched_size, p)); + if (pscore < 0) return 0; return pscore; } From 03c9e8abde40f081b11ad3d848f2972c8f6197fb Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 13 Feb 2019 12:27:16 +0100 Subject: [PATCH 010/471] [FIX] increase min score --- .../source/ANALYSIS/RNPXL/HyperScore.cpp | 2 +- src/utils/RNPxlSearch.cpp | 83 ++++++++++++------- 2 files changed, 54 insertions(+), 31 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp index 419bd319e78..8891f4c4b99 100644 --- a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp @@ -177,7 +177,7 @@ namespace OpenMS if (std::abs(theo_mz - exp_mz) < max_dist_dalton && exp_z == theo_z) { - dot_product += exp_spectrum[index].getIntensity() * theo_intensity /* * mass_error */; + dot_product += exp_spectrum[index].getIntensity() * theo_intensity; // fragment annotations in XL-MS data are more complex and do not start with the ion type, but the ion type always follows after a $ if ((*ion_names)[i][0] == 'y' || (*ion_names)[i].hasSubstring("$y")) { diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index a437b295dfa..6c31388827a 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -112,6 +112,8 @@ class RNPxlSearch : { } + static constexpr double MIN_HYPERSCORE = 0.1; // hit's with lower score than this will be neglected (usually 1 or 0 matches) + protected: void registerOptionsAndFlags_() override { @@ -1342,7 +1344,7 @@ class RNPxlSearch : PeptideIdentification pi; pi.setMetaValue("scan_index", static_cast(scan_index)); pi.setMetaValue("spectrum_reference", spec.getNativeID()); - pi.setScoreType("hyperscore"); + pi.setScoreType("RNPxlScore"); pi.setHigherScoreBetter(true); pi.setRT(spec.getRT()); pi.setMZ(spec.getPrecursors()[0].getMZ()); @@ -2007,8 +2009,8 @@ class RNPxlSearch : precursor_sub_score, a_ion_sub_score); - // bad score, likely wihout any single matching peak - if (total_loss_score < 0.01) { continue; } + // bad score or less then two peaks matching + if (total_loss_score < RNPxlSearch::MIN_HYPERSCORE || tlss_Morph < 2.0) { continue; } // add peptide hit AnnotatedHit ah; @@ -2144,7 +2146,7 @@ class RNPxlSearch : plss_err(1.0), plss_Morph(0), plss_modds(0), - score(0); + tlss_score(0); const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); PeakSpectrum & total_loss_spectrum = (exp_pc_charge < 3) ? total_loss_spectrum_z1 : total_loss_spectrum_z2; @@ -2155,7 +2157,7 @@ class RNPxlSearch : a_ion_sub_score_spectrum, precursor_sub_score_spectrum, immonium_sub_score_spectrum, - score, + tlss_score, tlss_MIC, tlss_err, tlss_Morph, @@ -2164,8 +2166,8 @@ class RNPxlSearch : precursor_sub_score, a_ion_sub_score); - // bad score, likely wihout any single matching peak - if (score < 0.01) { continue; } + // bad score or less then two peaks matching + if (tlss_score < MIN_HYPERSCORE || tlss_Morph < 2.0) { continue; } scorePartialLossFragments_(exp_spectrum, fragment_mass_tolerance, @@ -2179,12 +2181,15 @@ class RNPxlSearch : plss_err, plss_Morph, plss_modds); + + // less then two shifted peaks? + if (plss_Morph < 2.0) { continue; } // add peptide hit AnnotatedHit ah; ah.sequence = *cit; // copy StringView ah.peptide_mod_index = mod_pep_idx; - ah.total_loss_score = score; + ah.total_loss_score = tlss_score; ah.MIC = tlss_MIC; ah.err = tlss_err; ah.Morph = tlss_Morph; @@ -2270,7 +2275,7 @@ class RNPxlSearch : a_ion_sub_score); // no good hit - if (total_loss_score < 0.01) { continue; } + if (total_loss_score < MIN_HYPERSCORE) { continue; } // add peptide hit AnnotatedHit ah; @@ -2528,10 +2533,10 @@ class RNPxlSearch : total_loss_spectrum.getIntegerDataArrays()[0]); // bad score, likely wihout any single matching peak - if (total_loss_score < 0.01) + if (total_loss_score < MIN_HYPERSCORE) { // cap total loss error to a large value - float ft_da = fragment_mass_tolerance_unit_ppm ? fragment_mass_tolerance * 1e-6 * 1000.0 : fragment_mass_tolerance; + float ft_da = fragment_mass_tolerance_unit_ppm ? 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0 : 2.0 * fragment_mass_tolerance; if (tlss_err > ft_da) tlss_err = ft_da; return; } @@ -2547,8 +2552,10 @@ class RNPxlSearch : total_loss_spectrum.getIntegerDataArrays()[0]); tlss_MIC = tl_sub_scores.TIC != 0 ? tl_sub_scores.MIC / tl_sub_scores.TIC : 0; - tlss_err = tl_sub_scores.err; tlss_Morph = tl_sub_scores.score; + + // if we only have 1 or peaks assume some kind of average error to not underestimate the real error to much + tlss_err = tlss_Morph > 2 ? tl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; tlss_modds = matchOddsScore_(total_loss_spectrum, (int)tlss_Morph, // = number of matched peaks fragment_mass_tolerance, @@ -2639,8 +2646,9 @@ class RNPxlSearch : *pl_spec, pl_spec->getIntegerDataArrays()[0]); plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; - plss_err = pl_sub_scores.err; plss_Morph = pl_sub_scores.score; + // if we only have 1 peak assume some kind of average error to not underestimate the real error to much + plss_err = plss_Morph > 2 ? pl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; plss_modds = matchOddsScore_(*pl_spec, (int)plss_Morph, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm); } #ifdef DEBUG_RNPXLSEARCH @@ -3006,15 +3014,24 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( if (unmodified_sequence.has('K')) { const double immonium_ion2_mz = EmpiricalFormula("C5H10N1").getMonoWeight(); - spectrum.emplace_back(immonium_ion2_mz, 1.0); - spectrum_charge.emplace_back(1); - spectrum_annotation.emplace_back(String("iK(C5H10N1)")); + // only add special ios if there is not already a peak + if (spectrum.findNearest(immonium_ion2_mz, 1e-4) == -1) + { + spectrum.emplace_back(immonium_ion2_mz, 1.0); + spectrum_charge.emplace_back(1); + spectrum_annotation.emplace_back(String("iK(C5H10N1)")); + } // usually only observed without shift (A. Stuetzer) const double immonium_ion3_mz = EmpiricalFormula("C6H13N2O").getMonoWeight(); - spectrum.emplace_back(immonium_ion3_mz, 1.0); - spectrum_charge.emplace_back(1); - spectrum_annotation.emplace_back(String("iK(C6H13N2O)")); + // only add special ios if there is not already a peak + if (spectrum.findNearest(immonium_ion3_mz, 1e-4) == -1) + { + spectrum.emplace_back(immonium_ion3_mz, 1.0); + spectrum_charge.emplace_back(1); + spectrum_annotation.emplace_back(String("iK(C6H13N2O)")); + } + } } @@ -3231,6 +3248,7 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const S } partial_loss_spectrum.sortByPosition(); + } void RNPxlSearch::RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( @@ -3245,17 +3263,22 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( const double xl_mz = (fixed_and_variable_modified_peptide_weight + precursor_rna_weight + static_cast(charge) * Constants::PROTON_MASS_U) / static_cast(charge); - partial_loss_spectrum.push_back(Peak1D(xl_mz, 1.0)); - partial_loss_spectrum_charge.push_back(charge); - if (charge > 1) - { - partial_loss_spectrum_annotation.push_back(String("[M+") - + String(charge) + "H+" + precursor_rna_adduct + "]"); - } - else - { - partial_loss_spectrum_annotation.push_back(String("[M+H+") + precursor_rna_adduct + "]"); - } + + // only add special ions if there is not already a peak + if (partial_loss_spectrum.findNearest(xl_mz, 1e-4) == -1) + { + partial_loss_spectrum.push_back(Peak1D(xl_mz, 1.0)); + partial_loss_spectrum_charge.push_back(charge); + if (charge > 1) + { + partial_loss_spectrum_annotation.push_back(String("[M+") + + String(charge) + "H+" + precursor_rna_adduct + "]"); + } + else + { + partial_loss_spectrum_annotation.push_back(String("[M+H+") + precursor_rna_adduct + "]"); + } + } } int main(int argc, const char** argv) From f478990913cd03a8a26641aea192e5a1f107101a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 14 Feb 2019 09:25:09 +0100 Subject: [PATCH 011/471] [FEATURE] add normalized mass error score --- .../source/ANALYSIS/RNPXL/HyperScore.cpp | 14 ++++++-- src/openms/source/CHEMISTRY/AASequence.cpp | 8 +++-- src/utils/RNPxlSearch.cpp | 36 ++++++++++++++++--- 3 files changed, 49 insertions(+), 9 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp index 8891f4c4b99..96e3d4b8a04 100644 --- a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp @@ -37,6 +37,8 @@ #include #include +//#define DEBUG_HYPERSCORE 1 + using std::vector; namespace OpenMS @@ -111,8 +113,11 @@ namespace OpenMS const double yFact = logfactorial_(y_ion_count); const double bFact = logfactorial_(b_ion_count); const double hyperScore = log1p(dot_product) + yFact + bFact; - return hyperScore; - } + #ifdef DEBUG_HYPERSCORE + std::cout << "HyperScore/#y/#b: " << hyperScore << "/" << y_ion_count << "/" << b_ion_count << std::endl; + #endif + return hyperScore; + } double HyperScore::compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, @@ -170,7 +175,7 @@ namespace OpenMS const int theo_z = theo_charges[i]; #ifdef DEBUG_HYPERSCORE - if (exp_z != theo_z) std::cout << "exp_z != theo_z " << exp_z << "\t" << theo_z << std::endl; + if (exp_z != theo_z) std::cout << "exp_z != theo_z " << exp_z << "\t" << theo_z << std::endl; #endif // found peak match @@ -199,6 +204,9 @@ namespace OpenMS const double yFact = logfactorial_(y_ion_count); const double bFact = logfactorial_(b_ion_count); const double hyperScore = log1p(dot_product) + yFact + bFact; + #ifdef DEBUG_HYPERSCORE + std::cout << "HyperScore/#y/#b: " << hyperScore << "/" << y_ion_count << "/" << b_ion_count << std::endl; + #endif return hyperScore; } diff --git a/src/openms/source/CHEMISTRY/AASequence.cpp b/src/openms/source/CHEMISTRY/AASequence.cpp index 671524b3902..ae6b4ddca90 100644 --- a/src/openms/source/CHEMISTRY/AASequence.cpp +++ b/src/openms/source/CHEMISTRY/AASequence.cpp @@ -1111,7 +1111,9 @@ namespace OpenMS aas.c_term_mod_ = &(mod_db->getModification(term_mods[0], residue->getOneLetterCode(), ResidueModification::C_TERM)); return mod_end; } - LOG_WARN << "Warning: unknown C-terminal modification '" + mod + "' - adding it to the database" << std::endl; + LOG_WARN << "Warning: unknown C-terminal modification [+delta mass]'" + mod + + "' at residue: '" + residue->getOneLetterCode() + + "' - adding it to the database" << std::endl; } else // C-terminal mod specified by absolute mass [123.4] { @@ -1124,7 +1126,9 @@ namespace OpenMS aas.c_term_mod_ = &(mod_db->getModification(term_mods[0], residue->getOneLetterCode(), ResidueModification::C_TERM)); return mod_end; } - LOG_WARN << "Warning: unknown C-terminal modification '" + mod + "' - adding it to the database" << std::endl; + LOG_WARN << "Warning: unknown C-terminal modification [absolute mass] '" + mod + + "' at residue: '" + residue->getOneLetterCode() + + "' - adding it to the database" << std::endl; } } diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 6c31388827a..1dcf0beb97a 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -77,6 +77,8 @@ #include #include +#include + #include #include @@ -328,13 +330,16 @@ class RNPxlSearch : /// Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space /// floats need to be initialized to zero as default - struct AnnotatedHit + class AnnotatedHit { + public: StringView sequence; SignedSize peptide_mod_index = 0; // enumeration index of the non-RNA peptide modification Size rna_mod_index = 0; // index of the RNA modification int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment + float mass_error_p = 0; + static constexpr const char UNKNOWN_NUCLEOTIDE = '?'; char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE; // main score @@ -384,8 +389,8 @@ class RNPxlSearch : + 0.327 * ( 73.64 * ah.precursor_score - 0.821) + 0.748 * ( 22.014 * ah.marker_ions_score - 0.903) + 0.746 * ( 0.043 * ah.partial_loss_score - 0.472) - - 1.788 * ( 301.0 * ah.err - 1.771) - - 1.292 * (240.825 * ah.pl_err - 1.323) +/* - 1.788 * ( 301.0 * ah.err - 1.771) + - 1.292 * (240.825 * ah.pl_err - 1.323) */ + 2.324 * static_cast(isXL); /* old version return @@ -810,7 +815,7 @@ class RNPxlSearch : #endif peak_is_annotated.insert(aligned.second); - // only allow matching charges (if a fragment charge was assigned) + // only allow matching charges if (fragment_charge == charge) { RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); @@ -1379,6 +1384,7 @@ class RNPxlSearch : // determine RNA modification from index in map std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, ah.rna_mod_index); + ph.setMetaValue(String("RNPxl:mass_error_p"), ah.mass_error_p); ph.setMetaValue(String("RNPxl:total_loss_score"), ah.total_loss_score); ph.setMetaValue(String("RNPxl:immonium_score"), ah.immonium_score); ph.setMetaValue(String("RNPxl:precursor_score"), ah.precursor_score); @@ -1459,6 +1465,7 @@ class RNPxlSearch : feature_set << "isotope_error" << "RNPxl:score" + << "RNPxl:mass_error_p" << "RNPxl:total_loss_score" << "RNPxl:modds" << "RNPxl:immonium_score" @@ -1628,6 +1635,13 @@ class RNPxlSearch : Int min_precursor_charge = getIntOption_("precursor:min_charge"); Int max_precursor_charge = getIntOption_("precursor:max_charge"); double precursor_mass_tolerance = getDoubleOption_("precursor:mass_tolerance"); + + // true positives: assumed gaussian distribution of mass error + // with sigma^2 = precursor_mass_tolerance + boost::math::normal gaussian_mass_error(0.0, sqrt(precursor_mass_tolerance)); + // random: assumed uniform distribution of mass error + const float mass_error_prior_negatives = 1.0 / (2.0 * precursor_mass_tolerance); + bool precursor_mass_tolerance_unit_ppm = (getStringOption_("precursor:mass_tolerance_unit") == "ppm"); IntList precursor_isotopes = getIntList_("precursor:isotopes"); @@ -2012,8 +2026,12 @@ class RNPxlSearch : // bad score or less then two peaks matching if (total_loss_score < RNPxlSearch::MIN_HYPERSCORE || tlss_Morph < 2.0) { continue; } + const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; + // add peptide hit AnnotatedHit ah; + ah.mass_error_p = mass_error_score; ah.sequence = *cit; // copy StringView ah.peptide_mod_index = mod_pep_idx; ah.MIC = tlss_MIC; @@ -2185,8 +2203,13 @@ class RNPxlSearch : // less then two shifted peaks? if (plss_Morph < 2.0) { continue; } + const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; + // add peptide hit AnnotatedHit ah; + ah.mass_error_p = mass_error_score; + ah.sequence = *cit; // copy StringView ah.peptide_mod_index = mod_pep_idx; ah.total_loss_score = tlss_score; @@ -2277,8 +2300,13 @@ class RNPxlSearch : // no good hit if (total_loss_score < MIN_HYPERSCORE) { continue; } + const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; + // add peptide hit AnnotatedHit ah; + ah.mass_error_p = mass_error_score; + ah.sequence = *cit; // copy StringView ah.peptide_mod_index = mod_pep_idx; ah.total_loss_score = total_loss_score; From ae21d612f4269458e6da87f9b309902616f154fe Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 14 Feb 2019 16:41:00 +0100 Subject: [PATCH 012/471] [FIX] multiple + annotated, warning for xl mods at cterm --- .../RNPXL/RNPxlFragmentAnnotationHelper.cpp | 10 +++--- src/openms/source/CHEMISTRY/AASequence.cpp | 4 +-- .../TheoreticalSpectrumGenerator.cpp | 31 ++++++++++--------- src/utils/RNPxlSearch.cpp | 21 +++++++------ 4 files changed, 37 insertions(+), 29 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.cpp index c58b1cdc057..3c4e062361b 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.cpp @@ -110,7 +110,9 @@ namespace OpenMS String fas; for (auto & a : sorted) { - fas += String("(") + String::number(a.mz, 3) + "," + String::number(100.0 * a.intensity, 1) + ",\"" + a.annotation + "\")"; + fas += String("(") + String::number(a.mz, 3) + "," + + String::number(100.0 * a.intensity, 1) + ",\"" + + a.annotation + "\")"; if (&a != &sorted.back()) { fas += "|"; } } return fas; @@ -127,19 +129,19 @@ namespace OpenMS { if (!shifted_b_ions.empty()) { - const std::vector& fas_tmp = fragmentAnnotationDetailsToPHFA("b", shifted_b_ions); + const auto& fas_tmp = fragmentAnnotationDetailsToPHFA("b", shifted_b_ions); fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); } if (!shifted_y_ions.empty()) { - const std::vector& fas_tmp = fragmentAnnotationDetailsToPHFA("y", shifted_y_ions); + const auto& fas_tmp = fragmentAnnotationDetailsToPHFA("y", shifted_y_ions); fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); } if (!shifted_a_ions.empty()) { - const std::vector& fas_tmp = fragmentAnnotationDetailsToPHFA("a", shifted_a_ions); + const auto& fas_tmp = fragmentAnnotationDetailsToPHFA("a", shifted_a_ions); fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); } diff --git a/src/openms/source/CHEMISTRY/AASequence.cpp b/src/openms/source/CHEMISTRY/AASequence.cpp index ae6b4ddca90..844fff585dc 100644 --- a/src/openms/source/CHEMISTRY/AASequence.cpp +++ b/src/openms/source/CHEMISTRY/AASequence.cpp @@ -1111,7 +1111,7 @@ namespace OpenMS aas.c_term_mod_ = &(mod_db->getModification(term_mods[0], residue->getOneLetterCode(), ResidueModification::C_TERM)); return mod_end; } - LOG_WARN << "Warning: unknown C-terminal modification [+delta mass]'" + mod + LOG_DEBUG << "Warning: unknown C-terminal modification [+delta mass]'" + mod + "' at residue: '" + residue->getOneLetterCode() + "' - adding it to the database" << std::endl; } @@ -1126,7 +1126,7 @@ namespace OpenMS aas.c_term_mod_ = &(mod_db->getModification(term_mods[0], residue->getOneLetterCode(), ResidueModification::C_TERM)); return mod_end; } - LOG_WARN << "Warning: unknown C-terminal modification [absolute mass] '" + mod + LOG_DEBUG << "Warning: unknown C-terminal modification [absolute mass] '" + mod + "' at residue: '" + residue->getOneLetterCode() + "' - adding it to the database" << std::endl; } diff --git a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp index 0d810584501..165c568fff3 100644 --- a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp +++ b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp @@ -127,7 +127,10 @@ namespace OpenMS { } - void TheoreticalSpectrumGenerator::getSpectrum(PeakSpectrum & spectrum, const AASequence & peptide, Int min_charge, Int max_charge) const + void TheoreticalSpectrumGenerator::getSpectrum(PeakSpectrum & spectrum, + const AASequence & peptide, + Int min_charge, + Int max_charge) const { if (peptide.empty()) @@ -321,7 +324,7 @@ namespace OpenMS Peak1D p; IsotopeDistribution dist = ion.getFormula(res_type, charge).getIsotopeDistribution(CoarseIsotopePatternGenerator(max_isotope_)); - String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(ion.size()) + String(charge, '+'); + String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(ion.size()); double j(0.0); for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j) @@ -386,7 +389,7 @@ namespace OpenMS IsotopeDistribution dist = loss_ion.getIsotopeDistribution(CoarseIsotopePatternGenerator(max_isotope_)); // note: important to construct a string from char. If omitted it will perform pointer arithmetics on the "-" string literal - String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(ion.size()) + "-" + loss_name + String(charge, '+'); + String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(ion.size()) + "-" + loss_name; double j(0.0); for (IsotopeDistribution::ConstIterator iso = dist.begin(); iso != dist.end(); ++iso, ++j) @@ -407,7 +410,7 @@ namespace OpenMS if (add_metainfo_) { // note: important to construct a string from char. If omitted it will perform pointer arithmetics on the "-" string literal - String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(ion.size()) + "-" + loss_name + String(charge, '+'); + String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(ion.size()) + "-" + loss_name; ion_names.push_back(ion_name); charges.push_back(charge); } @@ -469,7 +472,7 @@ namespace OpenMS spectrum.push_back(p); if (add_metainfo_) { - String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(i + 1) + String(charge, '+'); + String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(i + 1); ion_names.push_back(ion_name); charges.push_back(charge); } @@ -523,7 +526,7 @@ namespace OpenMS spectrum.push_back(p); if (add_metainfo_) { - String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(peptide.size() - i) + String(charge, '+'); + String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(peptide.size() - i); ion_names.push_back(ion_name); charges.push_back(charge); } @@ -558,11 +561,11 @@ namespace OpenMS String ion_name; if (charge == 1) { - ion_name = "[M+H]+"; + ion_name = "[M+H]"; } else { - ion_name = "[M+" + String(charge) + "H]" + String(charge) + "+"; + ion_name = "[M+" + String(charge) + "H]"; } // precursor peak @@ -613,11 +616,11 @@ namespace OpenMS String ion_name; if (charge == 1) { - ion_name = "[M+H-H2O]+"; + ion_name = "[M+H-H2O]"; } else { - ion_name = "[M+" + String(charge) + "H-H2O]" + String(charge) + "+"; + ion_name = "[M+" + String(charge) + "H-H2O]"; } ion_names.push_back(ion_name); charges.push_back(charge); @@ -654,11 +657,11 @@ namespace OpenMS String ion_name; if (charge == 1) { - ion_name = "[M+H-NH3]+"; + ion_name = "[M+H-NH3]"; } else { - ion_name = "[M+" + String(charge) + "H-NH3]" + String(charge) + "+"; + ion_name = "[M+" + String(charge) + "H-NH3]"; } ion_names.push_back(ion_name); @@ -676,11 +679,11 @@ namespace OpenMS String ion_name; if (charge == 1) { - ion_name = "[M+H-NH3]+"; + ion_name = "[M+H-NH3]"; } else { - ion_name = "[M+" + String(charge) + "H-NH3]" + String(charge) + "+"; + ion_name = "[M+" + String(charge) + "H-NH3]"; } ion_names.push_back(ion_name); charges.push_back(charge); diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 1dcf0beb97a..c3281501fb2 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -382,16 +382,17 @@ class RNPxlSearch : static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) { - return - + 0.995 + return + + 0.995 + 7.142 * ( 0.058 * ah.total_loss_score - 0.900) + 0.802 * ( 33.35 * ah.immonium_score - 1.148) + 0.327 * ( 73.64 * ah.precursor_score - 0.821) + 0.748 * ( 22.014 * ah.marker_ions_score - 0.903) + 0.746 * ( 0.043 * ah.partial_loss_score - 0.472) -/* - 1.788 * ( 301.0 * ah.err - 1.771) - - 1.292 * (240.825 * ah.pl_err - 1.323) */ + - 1.788 * ( 301.0 * ah.err - 1.771) + - 1.292 * (240.825 * ah.pl_err - 1.323) + 2.324 * static_cast(isXL); + /* old version return 2.493 @@ -980,7 +981,7 @@ class RNPxlSearch : continue; } - for (vector >::const_iterator pair_it = alignment.begin(); pair_it != alignment.end(); ++pair_it) + for (auto pair_it = alignment.begin(); pair_it != alignment.end(); ++pair_it) { // only annotate experimental peaks with shift - i.e. do not annotated complete loss peaks again if (peak_is_annotated.find(pair_it->second) != peak_is_annotated.end()) { continue; } @@ -1109,7 +1110,7 @@ class RNPxlSearch : PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; fa.intensity = fragment_intensity; - fa.charge = 1; // for visualion charge is not really important so we set it to 1, TODO: read out charge from ion name and set here + fa.charge = 1; // TODO: read out charge from ion name and set here fa.annotation = ion_name; annotated_precursor_ions.push_back(fa); } @@ -1640,7 +1641,7 @@ class RNPxlSearch : // with sigma^2 = precursor_mass_tolerance boost::math::normal gaussian_mass_error(0.0, sqrt(precursor_mass_tolerance)); // random: assumed uniform distribution of mass error - const float mass_error_prior_negatives = 1.0 / (2.0 * precursor_mass_tolerance); + const double mass_error_prior_negatives = 1.0 / (2.0 * precursor_mass_tolerance); bool precursor_mass_tolerance_unit_ppm = (getStringOption_("precursor:mass_tolerance_unit") == "ppm"); IntList precursor_isotopes = getIntList_("precursor:isotopes"); @@ -2027,7 +2028,8 @@ class RNPxlSearch : if (total_loss_score < RNPxlSearch::MIN_HYPERSCORE || tlss_Morph < 2.0) { continue; } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; - const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) + / mass_error_prior_negatives; // add peptide hit AnnotatedHit ah; @@ -3304,7 +3306,8 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( } else { - partial_loss_spectrum_annotation.push_back(String("[M+H+") + precursor_rna_adduct + "]"); + partial_loss_spectrum_annotation.push_back(String("[M+H+") + + precursor_rna_adduct + "]"); } } } From 749011c9c966dab92296822c2a57e338a1973b5c Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 15 Feb 2019 13:25:54 +0100 Subject: [PATCH 013/471] [FIX] corrected another wrong annotation in TSG^ --- src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp index 165c568fff3..515e465dd77 100644 --- a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp +++ b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp @@ -600,7 +600,7 @@ namespace OpenMS } // loss peaks of the precursor - //loss of water + // loss of water EmpiricalFormula ion = peptide.getFormula(Residue::Full, charge) - EmpiricalFormula("H2O"); mono_pos = ion.getMonoWeight(); if (add_isotopes_) @@ -634,7 +634,7 @@ namespace OpenMS p.setIntensity(pre_int_H2O_); if (add_metainfo_) { - String ion_name("[M+H]-H2O" + String((Size)charge, '+')); + String ion_name("[M+H-H2O]"); ion_names.push_back(ion_name); charges.push_back(charge); } From a9ab66e9357d692f2a0bdb70d5259d6c256cf5ae Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 15 Feb 2019 13:26:32 +0100 Subject: [PATCH 014/471] [FIX] removed some duplicated peaks and enforce matching charges --- src/utils/RNPxlSearch.cpp | 280 +++++++++++++++----------------------- 1 file changed, 109 insertions(+), 171 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index c3281501fb2..e5f2f4fb550 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -46,6 +46,7 @@ #include #include #include +#include #include #include @@ -582,12 +583,6 @@ class RNPxlSearch : LOG_DEBUG << exp.size() << " : " << annotated_hits.size() << endl; #endif - SpectrumAlignment spectrum_aligner; - Param pa = spectrum_aligner.getParameters(); - pa.setValue("tolerance", fragment_mass_tolerance, "Defines the absolute (in Da) or relative (in ppm) tolerance in the alignment"); - pa.setValue("is_relative_tolerance", fragment_mass_tolerance_unit_ppm ? "true" : "false"); - spectrum_aligner.setParameters(pa); - // remove all but top n scoring for localization (usually all but the first one) #ifdef _OPENMP #pragma omp parallel for @@ -769,7 +764,17 @@ class RNPxlSearch : LOG_DEBUG << "Annotating ion (total loss spectrum): " << fixed_and_variable_modified_peptide.toString() << endl; #endif vector> alignment; - spectrum_aligner.getSpectrumAlignment(alignment, total_loss_spectrum, exp_spectrum); + + // align spectra (only allow matching charges) + DataArrays::FloatDataArray ppm_error_array; // not needed here but filled by alignment + OPXLSpectrumProcessingAlgorithms::getSpectrumAlignmentFastCharge(alignment, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + total_loss_spectrum, + exp_spectrum, + total_loss_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[0], + ppm_error_array); const PeakSpectrum::StringDataArray& total_loss_annotations = total_loss_spectrum.getStringDataArrays()[0]; const PeakSpectrum::IntegerDataArray& total_loss_charges = total_loss_spectrum.getIntegerDataArrays()[0]; @@ -791,129 +796,87 @@ class RNPxlSearch : { Size loss_first = ion_name.find_first_of('-'); // start of loss Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end + const bool ion_has_neutral_loss = (loss_first != string::npos); - if (loss_first != string::npos) // ion with neutral loss e.g. water + if (ion_has_neutral_loss) // ion with neutral loss e.g. water { - // only allow matching charges - if (fragment_charge == charge) - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - unshifted_loss_ions.push_back(fa); - peak_is_annotated.insert(aligned.second); - } + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + unshifted_loss_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); } - else - { - String ion_nr_string = ion_name.substr(1, charge_pos - 1); - Size ion_number = (Size)ion_nr_string.toInt(); - #ifdef DEBUG_RNPXLSEARCH - const AASequence& peptide_sequence = fixed_and_variable_modified_peptide.getSuffix(ion_number); - LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; - #endif - peak_is_annotated.insert(aligned.second); - - // only allow matching charges - if (fragment_charge == charge) + else // no neutral loss { + String ion_nr_string = ion_name.substr(1, charge_pos - 1); + Size ion_number = (Size)ion_nr_string.toInt(); RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); unshifted_y_ions[ion_number].push_back(d); - } - #ifdef DEBUG_RNPXLSEARCH - else - { - LOG_DEBUG << "Charge missmatch in alignment: " << ion_name << " at position: " << fragment_mz << " charge fragment: " << fragment_charge << " theo. charge: " << charge << endl; - } - #endif + #ifdef DEBUG_RNPXLSEARCH + const AASequence& peptide_sequence = fixed_and_variable_modified_peptide.getSuffix(ion_number); + LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; + #endif + peak_is_annotated.insert(aligned.second); } } else if (ion_name[0] == 'b') { Size loss_first = ion_name.find_first_of('-'); // start of loss Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end + const bool ion_has_neutral_loss = (loss_first != string::npos); - if (loss_first != string::npos) + if (ion_has_neutral_loss) { - // only allow matching charges - if (fragment_charge == charge) - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - unshifted_loss_ions.push_back(fa); - peak_is_annotated.insert(aligned.second); - } + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + unshifted_loss_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); } else { String ion_nr_string = ion_name.substr(1, charge_pos - 1); Size ion_number = (Size)ion_nr_string.toInt(); - #ifdef DEBUG_RNPXLSEARCH - const AASequence& peptide_sequence = aas.getPrefix(ion_number); - LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; - #endif - peak_is_annotated.insert(aligned.second); - - // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == charge) - { + #ifdef DEBUG_RNPXLSEARCH + const AASequence& peptide_sequence = aas.getPrefix(ion_number); + LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; + #endif RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); unshifted_b_ions[ion_number].push_back(d); - } - #ifdef DEBUG_RNPXLSEARCH - else - { - LOG_DEBUG << "Charge missmatch in alignment: " << ion_name << " at position: " << fragment_mz << " charge fragment: " << fragment_charge << " theo. charge: " << charge << endl; - } - #endif + peak_is_annotated.insert(aligned.second); } } else if (ion_name[0] == 'a') { Size loss_first = ion_name.find_first_of('-'); // start of loss Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end + const bool ion_has_neutral_loss = (loss_first != string::npos); - if (loss_first != string::npos) + if (ion_has_neutral_loss) { - // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == charge) - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - unshifted_loss_ions.push_back(fa); - peak_is_annotated.insert(aligned.second); - } + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + unshifted_loss_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); } else { String ion_nr_string = ion_name.substr(1, charge_pos - 1); auto ion_number = (Size)ion_nr_string.toInt(); - #ifdef DEBUG_RNPXLSEARCH - const AASequence& peptide_sequence = aas.getPrefix(ion_number); - LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; - #endif - peak_is_annotated.insert(aligned.second); - - // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == charge) - { + #ifdef DEBUG_RNPXLSEARCH + const AASequence& peptide_sequence = aas.getPrefix(ion_number); + LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; + #endif RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); unshifted_a_ions[ion_number].push_back(d); - } - #ifdef DEBUG_RNPXLSEARCH - else - { - LOG_DEBUG << "Charge missmatch in alignment: " << ion_name << " at position: " << fragment_mz << " charge fragment: " << fragment_charge << " theo. charge: " << charge << endl; - } - #endif + peak_is_annotated.insert(aligned.second); } } else if (ion_name.hasPrefix("[M+")) // precursor ion @@ -921,20 +884,20 @@ class RNPxlSearch : PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; fa.intensity = fragment_intensity; - fa.charge = 1; // for visualion charge is not really important so we set it to 0 + fa.charge = charge; fa.annotation = ion_name; - peak_is_annotated.insert(aligned.second); annotated_precursor_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); } else if (ion_name.hasPrefix("i")) // immonium ion { PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; fa.intensity = fragment_intensity; - fa.charge = 1; + fa.charge = charge; fa.annotation = ion_name; - peak_is_annotated.insert(aligned.second); annotated_immonium_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); } } @@ -969,8 +932,17 @@ class RNPxlSearch : ///////////////// // Align partial-loss-spectrum to the experimental measured one alignment.clear(); - - spectrum_aligner.getSpectrumAlignment(alignment, partial_loss_spectrum, exp_spectrum); + ppm_error_array.clear(); + + // align spectra (only allow matching charges) + OPXLSpectrumProcessingAlgorithms::getSpectrumAlignmentFastCharge(alignment, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + partial_loss_spectrum, + exp_spectrum, + total_loss_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[0], + ppm_error_array); const PeakSpectrum::StringDataArray& partial_loss_annotations = partial_loss_spectrum.getStringDataArrays()[0]; const PeakSpectrum::IntegerDataArray& partial_loss_charges = partial_loss_spectrum.getIntegerDataArrays()[0]; @@ -1016,18 +988,8 @@ class RNPxlSearch : ion_nr_string.substitute("+", ""); // remove one or multiple '+' auto ion_number = (Size)ion_nr_string.toInt(); - // only allow matching charges - if (fragment_charge == charge) - { - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); - shifted_y_ions[ion_number].push_back(d); - } - #ifdef DEBUG_RNPXLSEARCH - else - { - LOG_DEBUG << "Charge missmatch in alignment: " << ion_name << " at position: " << fragment_mz << " charge fragment: " << fragment_charge << " theo. charge: " << charge << endl; - } - #endif + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); + shifted_y_ions[ion_number].push_back(d); } else if (fragment_ion_name.hasPrefix("b")) { @@ -1036,18 +998,8 @@ class RNPxlSearch : ion_nr_string.substitute("+", ""); // remove one or multiple '+' auto ion_number = (Size)ion_nr_string.toInt(); - // only allow matching charges - if (fragment_charge == charge) - { - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); - shifted_b_ions[ion_number].push_back(d); - } - #ifdef DEBUG_RNPXLSEARCH - else - { - LOG_DEBUG << "Charge missmatch in alignment: " << ion_name << " at position: " << fragment_mz << " charge fragment: " << fragment_charge << " theo. charge: " << charge << endl; - } - #endif + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); + shifted_b_ions[ion_number].push_back(d); } else if (fragment_ion_name.hasPrefix("a")) { @@ -1056,18 +1008,8 @@ class RNPxlSearch : ion_nr_string.substitute("+", ""); // remove one or multiple '+' auto ion_number = (Size)ion_nr_string.toInt(); - // only allow matching charges (if a fragment charge was assigned) - if (fragment_charge == charge) - { - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); - shifted_a_ions[ion_number].push_back(d); - } - #ifdef DEBUG_RNPXLSEARCH - else - { - LOG_DEBUG << "Charge missmatch in alignment: " << ion_name << " at position: " << fragment_mz << " charge fragment: " << fragment_charge << " theo. charge: " << charge << endl; - } - #endif + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); + shifted_a_ions[ion_number].push_back(d); } else if (ion_name.hasPrefix(ANNOTATIONS_MARKER_ION_PREFIX)) { @@ -1080,12 +1022,6 @@ class RNPxlSearch : fa.annotation = ion_name; annotated_marker_ions.push_back(fa); } - #ifdef DEBUG_RNPXLSEARCH - else - { - LOG_DEBUG << "Charge missmatch in alignment: " << ion_name << " at position: " << fragment_mz << " charge fragment: " << fragment_charge << " theo. charge: " << 1 << endl; - } - #endif } else if (ion_name.hasPrefix("i")) { @@ -1098,19 +1034,13 @@ class RNPxlSearch : fa.annotation = ion_name; shifted_immonium_ions.push_back(fa); } - #ifdef DEBUG_RNPXLSEARCH - else - { - LOG_DEBUG << "Charge missmatch in alignment: " << ion_name << " at position: " << fragment_mz << " charge fragment: " << fragment_charge << " theo. charge: " << 1 << endl; - } - #endif } else if (ion_name.hasPrefix("[M+")) { PeptideHit::PeakAnnotation fa; fa.mz = fragment_mz; fa.intensity = fragment_intensity; - fa.charge = 1; // TODO: read out charge from ion name and set here + fa.charge = charge; fa.annotation = ion_name; annotated_precursor_ions.push_back(fa); } @@ -3177,18 +3107,6 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const S partial_loss_spectrum.getStringDataArrays().resize(1); // annotation PeakSpectrum::StringDataArray& partial_loss_spectrum_annotation = partial_loss_spectrum.getStringDataArrays()[0]; - // ADD: (mainly for ETD) MS2 precursor peaks of the MS1 adduct (total RNA) carrying peptide for all z <= precursor charge - for (int charge = 1; charge <= static_cast(precursor_charge); ++charge) - { - addPrecursorWithCompleteRNA_(fixed_and_variable_modified_peptide_weight, - precursor_rna_adduct, - precursor_rna_weight, - charge, - partial_loss_spectrum, - partial_loss_spectrum_charge, - partial_loss_spectrum_annotation); - } - // for all observable MS2 adducts ... for (Size i = 0; i != partial_loss_modification.size(); ++i) { @@ -3232,22 +3150,30 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const S { for (Size i = 0; i != partial_loss_template_z2.size(); ++i) { - Peak1D p = partial_loss_template_z2[i]; - p.setMZ(p.getMZ() + fragment_shift_mass / static_cast(z)); - shifted_series_peaks.push_back(p); - shifted_series_annotations.push_back(partial_loss_template_z2.getStringDataArrays()[0][i]); - shifted_series_charges.push_back(partial_loss_template_z2.getIntegerDataArrays()[0][i]); + // currently, also contains z=1 precursor peaks which we aleardy added before + if (partial_loss_template_z2.getIntegerDataArrays()[0][i] == z) + { + Peak1D p = partial_loss_template_z2[i]; + p.setMZ(p.getMZ() + fragment_shift_mass / static_cast(z)); + shifted_series_peaks.push_back(p); + shifted_series_annotations.push_back(partial_loss_template_z2.getStringDataArrays()[0][i]); + shifted_series_charges.push_back(partial_loss_template_z2.getIntegerDataArrays()[0][i]); + } } } else if (z == 3) { for (Size i = 0; i != partial_loss_template_z3.size(); ++i) { - Peak1D p = partial_loss_template_z3[i]; - p.setMZ(p.getMZ() + fragment_shift_mass / static_cast(z)); - shifted_series_peaks.push_back(p); - shifted_series_annotations.push_back(partial_loss_template_z3.getStringDataArrays()[0][i]); - shifted_series_charges.push_back(partial_loss_template_z3.getIntegerDataArrays()[0][i]); + // currently, also contains z=1 and 2 precursor peaks which we aleardy added before + if (partial_loss_template_z3.getIntegerDataArrays()[0][i] == z) + { + Peak1D p = partial_loss_template_z3[i]; + p.setMZ(p.getMZ() + fragment_shift_mass / static_cast(z)); + shifted_series_peaks.push_back(p); + shifted_series_annotations.push_back(partial_loss_template_z3.getStringDataArrays()[0][i]); + shifted_series_charges.push_back(partial_loss_template_z3.getIntegerDataArrays()[0][i]); + } } } else // don't consider fragment ions with charge >= 4 @@ -3277,6 +3203,18 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const S ); } + // ADD: (mainly for ETD) MS2 precursor peaks of the MS1 adduct (total RNA) carrying peptide for all z <= precursor charge + for (int charge = 1; charge <= static_cast(precursor_charge); ++charge) + { + addPrecursorWithCompleteRNA_(fixed_and_variable_modified_peptide_weight, + precursor_rna_adduct, + precursor_rna_weight, + charge, + partial_loss_spectrum, + partial_loss_spectrum_charge, + partial_loss_spectrum_annotation); + } + partial_loss_spectrum.sortByPosition(); } From 66f8dc5a99b735a3005f4a985cf5bcc0f72dcc90 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 18 Feb 2019 14:31:41 +0100 Subject: [PATCH 015/471] [FIX] added very conservative filtering --- src/utils/RNPxlSearch.cpp | 47 ++++++++++++++++++++++++++++++--------- 1 file changed, 37 insertions(+), 10 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 8b38049a421..6353e9bc9c2 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -116,7 +116,8 @@ class RNPxlSearch : } static constexpr double MIN_HYPERSCORE = 0.1; // hit's with lower score than this will be neglected (usually 1 or 0 matches) - + static constexpr double MIN_TOTAL_LOSS_IONS = 1; // minimum number of matches to unshifted ions + static constexpr double MIN_SHIFTED_IONS = 1; // minimum number of matches to shifted ions (applies to XLs only) protected: void registerOptionsAndFlags_() override { @@ -786,11 +787,13 @@ class RNPxlSearch : const Peak1D& fragment = exp_spectrum[fragment_index]; const double fragment_intensity = fragment.getIntensity(); // in percent (%) const double fragment_mz = fragment.getMZ(); - const int fragment_charge = exp_spectrum.getIntegerDataArrays().back()[fragment_index]; + const String& ion_name = total_loss_annotations[aligned.first]; const int charge = total_loss_charges[aligned.first]; + OPENMS_PRECONDITION(exp_spectrum.getIntegerDataArrays().back()[fragment_index] == charge, "Charges in alignment must match."); + // define which ion names are annotated if (ion_name[0] == 'y') { @@ -1956,7 +1959,13 @@ class RNPxlSearch : a_ion_sub_score); // bad score or less then two peaks matching - if (total_loss_score < RNPxlSearch::MIN_HYPERSCORE || tlss_Morph < 2.0) { continue; } + if (total_loss_score < MIN_HYPERSCORE + || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 + || tlss_modds < 1e-10 + || tlss_MIC < 0.01) + { + continue; + } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) @@ -2118,7 +2127,13 @@ class RNPxlSearch : a_ion_sub_score); // bad score or less then two peaks matching - if (tlss_score < MIN_HYPERSCORE || tlss_Morph < 2.0) { continue; } + if (tlss_score < MIN_HYPERSCORE + || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 + || tlss_modds < 1e-10 + || tlss_MIC < 0.01) + { + continue; + } scorePartialLossFragments_(exp_spectrum, fragment_mass_tolerance, @@ -2132,9 +2147,17 @@ class RNPxlSearch : plss_err, plss_Morph, plss_modds); - + + const double total_MIC = tlss_MIC + plss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; // less then two shifted peaks? - if (plss_Morph < 2.0) { continue; } + if ( partial_loss_sub_score < MIN_HYPERSCORE // at least one peak with 10% of max intensity + || plss_Morph < MIN_SHIFTED_IONS + 1.0 // > 1 shifted peaks + || plss_modds < 1e-10 + || total_MIC < 0.01 // less than 1% explained peaks + ) + { + continue; + } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; @@ -2158,8 +2181,7 @@ class RNPxlSearch : ah.precursor_score = precursor_sub_score; ah.a_ion_score = a_ion_sub_score; ah.cross_linked_nucleotide = cross_linked_nucleotide; - ah.total_MIC = tlss_MIC + plss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; - + ah.total_MIC = total_MIC; // scores from shifted peaks ah.marker_ions_score = marker_ions_sub_score; ah.partial_loss_score = partial_loss_sub_score; @@ -2230,8 +2252,13 @@ class RNPxlSearch : precursor_sub_score, a_ion_sub_score); - // no good hit - if (total_loss_score < MIN_HYPERSCORE) { continue; } + // bad score or less then two peaks matching + if (total_loss_score < MIN_HYPERSCORE + || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 + || tlss_modds < 1e-10) + { + continue; + } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; From ebbd6ef57c96bb13aac4805efc56ed108ebe44ce Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 21 Feb 2019 16:28:53 +0100 Subject: [PATCH 016/471] [FEATURE] new slow scoring model (2 models) --- src/utils/RNPxlSearch.cpp | 146 +++++++++++++++++++++----------------- 1 file changed, 79 insertions(+), 67 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 6353e9bc9c2..e3ba0914239 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -79,6 +79,7 @@ #include #include #include +#include #include @@ -384,8 +385,63 @@ class RNPxlSearch : static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) { - return - + 0.995 +/* + coeff. std. err. Z-score P>|z| +not isXL: +1 RNPxl:total_loss_score 0.21721652155697285 0.09483942249623674 2.2903610739046 0.022000394091310493 +1 RNPxl:mass_error_p 1.9988345415208777 0.5320970905622918 3.756522215538927 1.7229098345827865E-4 +1 RNPxl:modds 0.5842539236790404 0.14707508807450823 3.972487328262264 7.112602099945686E-5 +1 RNPxl:total_MIC 4.059968526608637 0.6997810753887223 5.801769538213591 6.561872156751747E-9 +1 Constant -6.486416409280039 1.0530367515627284 -6.159724624666768 7.287158654278869E-10 + + isXL: + coeff. std. err. Z-score P>|z| +RNPxl:pl_MIC 2.3319284783288805 1.443968593532589 1.614944042947601 0.10632281328213189 +RNPxl:pl_Morph -0.1821314450150078 0.0992607992067629 -1.8348778820088194 0.06652378554713212 +RNPxl:mass_error_p 1.2107674392113372 0.6479149468312813 1.8687135481790702 0.06166267808238679 +RNPxl:total_loss_score 0.25318342707227187 0.11026025896332549 2.2962346492990293 0.02166246839013919 +RNPxl:modds 0.5446999629799386 0.21771187712636128 2.501930396125295 0.012351820599275531 +RNPxl:partial_loss_score 0.12472562244230834 0.04757766801488459 2.6215160945527667 0.008753962882873556 +RNPxl:Morph 0.4688059636415974 0.14790453990151833 3.169652290279595 0.0015262145546381944 +RNPxl:MIC 4.0386886051238 1.161533977368853 3.477030103133424 5.070008902814394E-4 +Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.5283262211340798E-7 + +*/ + + if (!isXL) + { + return - 6.486416409280039 + + 4.059968526608637 * ah.total_MIC + + 0.5842539236790404 * ah.modds + + 0.21721652155697285 * ah.total_loss_score + + 1.9988345415208777 * ah.mass_error_p; + } + else + { + return - 6.648631037190969 + + 0.4688059636415974 * ah.Morph + + 4.0386886051238 * ah.MIC + + 0.5446999629799386 * ah.modds + + 0.25318342707227187 * ah.total_loss_score + + 0.12472562244230834 * ah.partial_loss_score + + 1.2107674392113372 * ah.mass_error_p + + 2.3319284783288805 * ah.pl_MIC + - 0.1821314450150078 * ah.pl_Morph; + } +// return ah.total_loss_score + ah.total_MIC + ah.mass_error_p / 3.0; +/* + return - 4.2 + + 1.995 * ah.total_MIC + + 1.115 * ah.mass_error_p + + 0.504 * ah.total_loss_score + - 0.021 * ah.Morph + - 0.011 * ah.modds + + 0.084 * ah.partial_loss_score + - 0.244 * ah.pl_Morph + - 1.077 * static_cast(isXL); +*/ +/* + return + 0.995 + 7.142 * ( 0.058 * ah.total_loss_score - 0.900) + 0.802 * ( 33.35 * ah.immonium_score - 1.148) + 0.327 * ( 73.64 * ah.precursor_score - 0.821) @@ -394,7 +450,7 @@ class RNPxlSearch : - 1.788 * ( 301.0 * ah.err - 1.771) - 1.292 * (240.825 * ah.pl_err - 1.323) + 2.324 * static_cast(isXL); - +*/ /* old version return 2.493 @@ -2129,8 +2185,8 @@ class RNPxlSearch : // bad score or less then two peaks matching if (tlss_score < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_modds < 1e-10 - || tlss_MIC < 0.01) + || tlss_MIC < 0.01 + || tlss_modds < 1e-10) { continue; } @@ -2149,16 +2205,15 @@ class RNPxlSearch : plss_modds); const double total_MIC = tlss_MIC + plss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; - // less then two shifted peaks? - if ( partial_loss_sub_score < MIN_HYPERSCORE // at least one peak with 10% of max intensity + // less then two shifted peaks? seems to throw out some good hits ??? +/* if ( partial_loss_sub_score < MIN_HYPERSCORE // at least one peak with 10% of max intensity || plss_Morph < MIN_SHIFTED_IONS + 1.0 // > 1 shifted peaks - || plss_modds < 1e-10 || total_MIC < 0.01 // less than 1% explained peaks ) { continue; } - +*/ const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; @@ -2252,10 +2307,13 @@ class RNPxlSearch : precursor_sub_score, a_ion_sub_score); - // bad score or less then two peaks matching + const double total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; + + // super bad score if (total_loss_score < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_modds < 1e-10) + || tlss_modds < 1e-10 + || total_MIC < 0.01) { continue; } @@ -2278,13 +2336,13 @@ class RNPxlSearch : ah.precursor_score = precursor_sub_score; ah.a_ion_score = a_ion_sub_score; - ah.total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; + ah.total_MIC = total_MIC; ah.rna_mod_index = rna_mod_index; ah.isotope_error = isotope_error; // simple combined score in fast scoring: - ah.score = total_loss_score + ah.total_MIC; + ah.score = total_loss_score + ah.total_MIC + mass_error_score / 3.0; #ifdef DEBUG_RNPXLSEARCH LOG_DEBUG << "best score in pre-score: " << score << endl; @@ -2440,62 +2498,19 @@ class RNPxlSearch : static double matchOddsScore_( const PeakSpectrum& theoretical_spec, - const Size matched_size, - const double fragment_mass_tolerance, - const bool fragment_mass_tolerance_unit_ppm) + const Size matched_size) { - static AScore a_score_algorithm; const Size N = theoretical_spec.size(); if (matched_size < 1 || N < 1) { return 0; } - // compute p score as e.g. in the AScore implementation or Andromeda const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see ThresholdMower) - const double pscore = -10.0 * log10(a_score_algorithm.computeCumulativeScore(N, matched_size, p)); - if (pscore < 0) return 0; - return pscore; - } + const double pscore = boost::math::ibeta(matched_size + 1, N - matched_size, p); + if (pscore <= std::numeric_limits::min()) return -log10(std::numeric_limits::min()); + const double minusLog10p1pscore = -log10(pscore); + return minusLog10p1pscore; + } -/* - static double matchOddsScore_( - const PeakSpectrum& theoretical_spec, - const Size matched_size, - const double fragment_mass_tolerance, - const bool fragment_mass_tolerance_unit_ppm) - { - using boost::math::binomial; - Size theo_size = theoretical_spec.size(); - - if (matched_size < 1 || theo_size < 1) { return 0; } - - double range = theoretical_spec[theo_size-1].getMZ() - theoretical_spec[0].getMZ(); - - // Compute fragment tolerance in Da for the mean of MZ values, if tolerance in ppm (rough approximation) - double mean = 0.0; - for (Size i = 0; i < theo_size; ++i) { mean += theoretical_spec[i].getMZ(); } - mean /= (double)theo_size; - double tolerance_Th = fragment_mass_tolerance_unit_ppm ? mean * 1e-6 * fragment_mass_tolerance : fragment_mass_tolerance; - - // A priori probability of a random match given info about the theoretical spectrum - long double a_priori_p = (1 - ( pow( (1 - 2 * tolerance_Th / (0.5 * range)), static_cast(theo_size)))); - - long double match_odds(0); - - binomial flip(theo_size, a_priori_p); - // min double number to avoid 0 values, causing scores with the value "inf" - match_odds = -log(1 - cdf(flip, (long double)matched_size) + std::numeric_limits::min()); - - // score lower than 0 does not make sense, but can happen if cfd = 0, -log( 1 + min() ) < 0 - if (match_odds >= 0.0) - { - return (double)match_odds; - } - else - { - return 0; - } - } -*/ // determine main score and sub scores of peaks without shifts void scoreTotalLossFragments_(const PeakSpectrum &exp_spectrum, const PeakSpectrum &total_loss_spectrum, @@ -2544,10 +2559,7 @@ class RNPxlSearch : // if we only have 1 or peaks assume some kind of average error to not underestimate the real error to much tlss_err = tlss_Morph > 2 ? tl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - tlss_modds = matchOddsScore_(total_loss_spectrum, - (int)tlss_Morph, // = number of matched peaks - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm); + tlss_modds = matchOddsScore_(total_loss_spectrum, (int)tlss_Morph); // (int)Morph == number of matched peaks if (!immonium_sub_score_spectrum.empty()) { @@ -2637,7 +2649,7 @@ class RNPxlSearch : plss_Morph = pl_sub_scores.score; // if we only have 1 peak assume some kind of average error to not underestimate the real error to much plss_err = plss_Morph > 2 ? pl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - plss_modds = matchOddsScore_(*pl_spec, (int)plss_Morph, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm); + plss_modds = matchOddsScore_(*pl_spec, (int)plss_Morph); } #ifdef DEBUG_RNPXLSEARCH LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; From 537429bc693c637be2b2c1b7876578a72708d08e Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 25 Feb 2019 17:07:25 +0100 Subject: [PATCH 017/471] [FEATURE] use extensive scoring as postprocessing in fast scoring --- src/utils/RNPxlSearch.cpp | 184 ++++++++++++++++++++++++++++++++------ 1 file changed, 159 insertions(+), 25 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index e3ba0914239..322df8f0039 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -148,7 +148,7 @@ class RNPxlSearch : registerIntOption_("precursor:max_charge", "", 5, "Maximum precursor charge to be considered.", false, false); // consider one before annotated monoisotopic peak and the annotated one - IntList isotopes = {0, 1}; + IntList isotopes = {0}; registerIntList_("precursor:isotopes", "", isotopes, "Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak)", false, false); registerTOPPSubsection_("fragment", "Fragments (Product Ion) Options"); @@ -410,7 +410,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 if (!isXL) { - return - 6.486416409280039 + return - 6.486416409280039 + 4.059968526608637 * ah.total_MIC + 0.5842539236790404 * ah.modds + 0.21721652155697285 * ah.total_loss_score @@ -418,7 +418,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 } else { - return - 6.648631037190969 + return - 6.648631037190969 + 0.4688059636415974 * ah.Morph + 4.0386886051238 * ah.MIC + 0.5446999629799386 * ah.modds @@ -594,7 +594,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 static void generatePartialLossSpectrum(const String& unmodified_sequence, const double& fixed_and_variable_modified_peptide_weight, const String& precursor_rna_adduct, - const double& precursor_rna_weight, + const double& precursor_rna_mass, const int& precursor_charge, const vector& partial_loss_modification, const PeakSpectrum& patial_loss_template_z1, @@ -603,7 +603,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 PeakSpectrum& partial_loss_spectrum); static void addPrecursorWithCompleteRNA_(const double fixed_and_variable_modified_peptide_weight, const String & precursor_rna_adduct, - const double precursor_rna_weight, + const double precursor_rna_mass, const int charge, PeakSpectrum & partial_loss_spectrum, MSSpectrum::IntegerDataArray & partial_loss_spectrum_charge, @@ -656,6 +656,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 // If we did a (total-loss) only fast scoring, PSMs were not associated with a nucleotide. // To make the localization code work for both fast and slow (all-shifts) scoring, // we copy PSMs for every cross-linkable nucleotide present in the precursor. + // Then we recalculate the XL specific scores not conisdered in fast scoring if (fast_scoring_) { #ifdef _OPENMP @@ -665,7 +666,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 { vector new_hits; - // for each PSM + // for each PSM of this spectrum for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) { // determine RNA on precursor from index in map @@ -673,24 +674,157 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 std::advance(mod_combinations_it, annotated_hits[scan_index][i].rna_mod_index); const String precursor_rna_adduct = *mod_combinations_it->second.begin(); const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; - - // just copy non-cross-linked peptide PSMs + if (precursor_rna_adduct == "none") { new_hits.push_back(annotated_hits[scan_index][i]); - continue; } - - // if we have a cross-link, copy PSM information for each cross-linkable nucleotides - for (auto const & c : feasible_MS2_adducts) + else { - AnnotatedHit a(annotated_hits[scan_index][i]); - a.cross_linked_nucleotide = c.first; // nucleotide - new_hits.push_back(a); + // if we have a cross-link, copy PSM information for each cross-linkable nucleotides + for (auto const & c : feasible_MS2_adducts) + { + AnnotatedHit a(annotated_hits[scan_index][i]); + a.cross_linked_nucleotide = c.first; // nucleotide + new_hits.push_back(a); + } } } annotated_hits[scan_index].swap(new_hits); } + + // fill in values of slow scoring so they can be used in percolator + for (Size scan_index = 0; scan_index != annotated_hits.size(); ++scan_index) + { + // for each PSM of this spectrum + for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) + { + AnnotatedHit& ah = annotated_hits[scan_index][i]; + + // reconstruct fixed and variable modified peptide sequence (without RNA) + const String& unmodified_sequence = ah.sequence.getString(); + AASequence aas = AASequence::fromString(unmodified_sequence); + vector all_modified_peptides; + ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications.begin(), fixed_modifications.end(), aas); + ModifiedPeptideGenerator::applyVariableModifications(variable_modifications.begin(), variable_modifications.end(), aas, max_variable_mods_per_peptide, all_modified_peptides); + AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; + double current_peptide_mass_without_RNA = fixed_and_variable_modified_peptide.getMonoWeight(); + + // determine RNA on precursor from index in map + auto mod_combinations_it = mm.mod_combinations.begin(); + std::advance(mod_combinations_it, ah.rna_mod_index); + const String precursor_rna_adduct = *mod_combinations_it->second.begin(); + const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; + const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; + const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); + + if (precursor_rna_adduct == "none") + { + ah.score = RNPxlSearch::calculateCombinedScore(ah, false); + continue; + } + + // determine current nucleotide and associated partial losses + vector partial_loss_modification; + for (auto const & nuc_2_adducts : feasible_MS2_adducts) + { + if(nuc_2_adducts.first == ah.cross_linked_nucleotide) + { + partial_loss_modification = nuc_2_adducts.second; + } + } + + // TODO: not needed to generate all templates (but will make not much of a difference + // as this is only done a few thousand times during post-scoring). That way, + // the code is basically the same as in the main scoring loop. + PeakSpectrum partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3; + + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); + + PeakSpectrum marker_ions_sub_score_spectrum_z1, + partial_loss_spectrum_z1, + partial_loss_spectrum_z2; + + // nucleotide is associated with certain NA-related fragment losses? + if (!partial_loss_modification.empty()) + { + // shifted b- / y- / a-ions + // generate shifted_immonium_ions_sub_score_spectrum.empty + RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, + current_peptide_mass_without_RNA, + precursor_rna_adduct, + precursor_rna_mass, + 1, + partial_loss_modification, + partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3, + partial_loss_spectrum_z1); + for (auto& n : partial_loss_spectrum_z1.getStringDataArrays()[0]) { n[0] = 'y'; } // hyperscore hack + + RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, + current_peptide_mass_without_RNA, + precursor_rna_adduct, + precursor_rna_mass, + 2, // don't know the charge of the precursor at that point + partial_loss_modification, + partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3, + partial_loss_spectrum_z2); + for (auto& n : partial_loss_spectrum_z2.getStringDataArrays()[0]) { n[0] = 'y'; } // hyperscore hack + } + + // add shifted marker ions + marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation + RNPxlFragmentIonGenerator::addMS2MarkerIons( + marker_ions, + marker_ions_sub_score_spectrum_z1, + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0], + marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); + + const PeakSpectrum& exp_spectrum = exp[scan_index]; + float partial_loss_sub_score(0), + marker_ions_sub_score(0), + plss_MIC(0), + plss_err(1.0), + plss_Morph(0), + plss_modds(0), + tlss_score(0); + + scorePartialLossFragments_(exp_spectrum, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + partial_loss_spectrum_z1, + partial_loss_spectrum_z2, + marker_ions_sub_score_spectrum_z1, + partial_loss_sub_score, + marker_ions_sub_score, + plss_MIC, + plss_err, + plss_Morph, + plss_modds); + + + // fill in missing scores not considered in fast scoring + ah.pl_MIC = plss_MIC; + ah.pl_err = plss_err; + ah.pl_Morph = plss_Morph; + ah.pl_modds = plss_modds; + // add extra matched ion current + ah.total_MIC += plss_MIC; + // scores from shifted peaks + ah.marker_ions_score = marker_ions_sub_score; + ah.partial_loss_score = partial_loss_sub_score; + // combined score + ah.score = RNPxlSearch::calculateCombinedScore(ah, true); + } + } } #ifdef _OPENMP @@ -727,7 +861,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, a.rna_mod_index); const String precursor_rna_adduct = *mod_combinations_it->second.begin(); - const double precursor_rna_weight = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); + const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); // we don't localize on non-cross-links if (precursor_rna_adduct == "none") { continue; } @@ -787,7 +921,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, fixed_and_variable_modified_peptide_weight, precursor_rna_adduct, - precursor_rna_weight, + precursor_rna_mass, precursor_charge, partial_loss_modification, partial_loss_template_z1, @@ -1928,8 +2062,8 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 rna_mod_it != mm.mod_masses.end(); ++rna_mod_it, ++rna_mod_index) { - const double precursor_rna_weight = rna_mod_it->second; - const double current_peptide_mass = current_peptide_mass_without_RNA + precursor_rna_weight; // add RNA mass + const double precursor_rna_mass = rna_mod_it->second; + const double current_peptide_mass = current_peptide_mass_without_RNA + precursor_rna_mass; // add RNA mass // TODO: const char xl_nucleotide; // can be none // determine MS2 precursors that match to the current peptide mass @@ -2112,7 +2246,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, current_peptide_mass_without_RNA, precursor_rna_adduct, - precursor_rna_weight, + precursor_rna_mass, 1, partial_loss_modification, partial_loss_template_z1, @@ -2124,7 +2258,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, current_peptide_mass_without_RNA, precursor_rna_adduct, - precursor_rna_weight, + precursor_rna_mass, 2, // don't know the charge of the precursor at that point partial_loss_modification, partial_loss_template_z1, @@ -3133,7 +3267,7 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::addShiftedImmoniumIons(const String void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const String &unmodified_sequence, const double &fixed_and_variable_modified_peptide_weight, const String &precursor_rna_adduct, - const double &precursor_rna_weight, + const double &precursor_rna_mass, const int &precursor_charge, const vector &partial_loss_modification, const PeakSpectrum& partial_loss_template_z1, @@ -3249,7 +3383,7 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const S { addPrecursorWithCompleteRNA_(fixed_and_variable_modified_peptide_weight, precursor_rna_adduct, - precursor_rna_weight, + precursor_rna_mass, charge, partial_loss_spectrum, partial_loss_spectrum_charge, @@ -3263,13 +3397,13 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const S void RNPxlSearch::RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( const double fixed_and_variable_modified_peptide_weight, const String &precursor_rna_adduct, - const double precursor_rna_weight, + const double precursor_rna_mass, const int charge, PeakSpectrum &partial_loss_spectrum, MSSpectrum::IntegerDataArray &partial_loss_spectrum_charge, MSSpectrum::StringDataArray &partial_loss_spectrum_annotation) { - const double xl_mz = (fixed_and_variable_modified_peptide_weight + precursor_rna_weight + + const double xl_mz = (fixed_and_variable_modified_peptide_weight + precursor_rna_mass + static_cast(charge) * Constants::PROTON_MASS_U) / static_cast(charge); From bd580da1be4fbe4e9f8bbae5689dd886b498d3a8 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 26 Feb 2019 12:11:32 +0100 Subject: [PATCH 018/471] [FEATURE] add iterator-based int from string --- .../OpenMS/DATASTRUCTURES/StringUtils.h | 12 ++++ .../source/DATASTRUCTURES/StringUtils.cpp | 7 +-- .../openms/source/StringUtils_test.cpp | 55 +++++++++++++++++++ 3 files changed, 70 insertions(+), 4 deletions(-) diff --git a/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h b/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h index 2a4435512dc..bb43355e35f 100644 --- a/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h +++ b/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h @@ -828,6 +828,17 @@ namespace OpenMS return boost::spirit::qi::parse(begin, end, parse_double_, target); } + /// Reads an int from an iterator position. + /// The begin iterator is modified (advanced) if parsing was successful. + /// The @p target only contains a valid result if the functions returns true (i.e. parsing succeeded). + /// Whitespaces before and after the double are NOT consumed! + template + static bool extractInt(IteratorT& begin, const IteratorT& end, int& target) + { + // qi::parse() does not consume whitespace before or after the int (qi::parse_phrase() would). + return boost::spirit::qi::parse(begin, end, parse_int_, target); + } + static String& toUpper(String & this_s) { @@ -956,6 +967,7 @@ namespace OpenMS // (the original Boost implementation has a bug, see https://svn.boost.org/trac/boost/ticket/6955) static boost::spirit::qi::real_parser > parse_double_; static boost::spirit::qi::real_parser > parse_float_; + static boost::spirit::qi::int_parser<> parse_int_; }; diff --git a/src/openms/source/DATASTRUCTURES/StringUtils.cpp b/src/openms/source/DATASTRUCTURES/StringUtils.cpp index 4f3174934d6..3a9b7ad48dc 100644 --- a/src/openms/source/DATASTRUCTURES/StringUtils.cpp +++ b/src/openms/source/DATASTRUCTURES/StringUtils.cpp @@ -36,8 +36,7 @@ namespace OpenMS { - - boost::spirit::qi::real_parser > StringUtils::parse_double_ = boost::spirit::qi::real_parser >(); - boost::spirit::qi::real_parser > StringUtils::parse_float_ = boost::spirit::qi::real_parser >(); - + boost::spirit::qi::real_parser > StringUtils::parse_double_ = boost::spirit::qi::real_parser >(); + boost::spirit::qi::real_parser > StringUtils::parse_float_ = boost::spirit::qi::real_parser >(); + boost::spirit::qi::int_parser<> StringUtils::parse_int_ = boost::spirit::qi::int_parser<>(); } diff --git a/src/tests/class_tests/openms/source/StringUtils_test.cpp b/src/tests/class_tests/openms/source/StringUtils_test.cpp index a16540cb514..563557e27fb 100644 --- a/src/tests/class_tests/openms/source/StringUtils_test.cpp +++ b/src/tests/class_tests/openms/source/StringUtils_test.cpp @@ -336,6 +336,61 @@ START_SECTION((template static bool extractDouble(IteratorT } END_SECTION +START_SECTION((template static bool extractInt(IteratorT& begin, const IteratorT& end, int& target))) +{ + int i; + { + std::string ss("12345 "); + auto it = ss.begin(); + TEST_EQUAL(StringUtils::extractInt(it, ss.end(), i), true); + TEST_EQUAL(i, 12345) + TEST_EQUAL((int)std::distance(ss.begin(), it), 5); // was the iterator advanced? + } + + { + std::string ss("+1234!"); + auto it = ss.begin(); + TEST_EQUAL(StringUtils::extractInt(it, ss.end(), i), true); + TEST_EQUAL(i, 1234) + TEST_EQUAL((int)std::distance(ss.begin(), it), 5); // was the iterator advanced? + } + { + i = 0; + std::string ss(" -123"); + auto it = ss.begin(); + TEST_EQUAL(StringUtils::extractInt(it, ss.end(), i), false); + TEST_EQUAL(i, 0) + TEST_EQUAL((int)std::distance(ss.begin(), it), 0); // was the iterator advanced? + } + { + std::string ss("y15++"); + auto it = ss.begin() + 1; + TEST_EQUAL(StringUtils::extractInt(it, ss.end(), i), true); + TEST_EQUAL(i, 15) + TEST_EQUAL((int)std::distance(ss.begin(), it), 3); // was the iterator advanced? + } + { + // try two ints in a single stream (should stop after the first) + std::string ss("-5 9"); + auto it = ss.begin(); + TEST_EQUAL(StringUtils::extractInt(it, ss.end(), i), true); + TEST_EQUAL(i, -5) + TEST_EQUAL((int)std::distance(ss.begin(), it), 2); // was the iterator advanced? + auto it2 = ss.begin() + 3; + TEST_EQUAL(StringUtils::extractInt(it2, ss.end(), i), true); + TEST_EQUAL(i, 9) + TEST_EQUAL((int)std::distance(ss.begin(), it2), 4); // was the iterator advanced? + } + { + std::string ss("!noNumber"); + auto it = ss.begin(); + TEST_EQUAL(StringUtils::extractInt(it, ss.end(), i), false); + TEST_EQUAL((int)std::distance(ss.begin(), it), 0); // was the iterator advanced? + } +} +END_SECTION + + START_SECTION((static String& toUpper(String &this_s))) { // TODO From 729945356b702062a6e81f5ea7b5156b19d571cc Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 27 Feb 2019 18:05:59 +0100 Subject: [PATCH 019/471] [FEATURE] optimize by scoring all at fragments at once --- .../OpenMS/ANALYSIS/RNPXL/HyperScore.h | 21 + .../source/ANALYSIS/RNPXL/HyperScore.cpp | 140 ++- src/utils/RNPxlSearch.cpp | 932 +++++++++++++----- 3 files changed, 842 insertions(+), 251 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h index b25d5c60dc7..cfe81e2f70c 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h @@ -84,6 +84,27 @@ struct OPENMS_DLLAPI HyperScore const PeakSpectrum& theo_spectrum, const DataArrays::IntegerDataArray& theo_charges); + /* @brief compute the (ln transformed) X!Tandem HyperScore only matching peaks that match in charge + * 1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated + * 2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions + * @note Peak intensities of the theoretical spectrum are typically 1 or TIC normalized, but can also be e.g. ion probabilities + * @param fragment_mass_tolerance mass tolerance applied left and right of the theoretical spectrum peak position + * @param fragment_mass_tolerance_unit_ppm Unit of the mass tolerance is: Thomson if false, ppm if true + * @param exp_spectrum measured spectrum + * @param exp_charges charges of measured peaks + * @param theo_spectrum theoretical spectrum Peaks need to contain an ion annotation as provided by TheoreticalSpectrumGenerator. + * @param theo_charges charges of theoretical peaks + * @param intensity_sum summed intensity for observed bond indices (e.g., b3=123 -> intensity_sum[2]=123) + * Note: intensity_sum must be zeroed and of size #AA in peptide + */ + static double compute(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const DataArrays::IntegerDataArray& exp_charges, + const PeakSpectrum& theo_spectrum, + const DataArrays::IntegerDataArray& theo_charges, + std::vector& intensity_sum); + private: // helper to compute the log factorial static double logfactorial_(UInt x); diff --git a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp index 96e3d4b8a04..2f9e77cef98 100644 --- a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp @@ -36,6 +36,7 @@ #include #include +#include //#define DEBUG_HYPERSCORE 1 @@ -182,10 +183,10 @@ namespace OpenMS if (std::abs(theo_mz - exp_mz) < max_dist_dalton && exp_z == theo_z) { - dot_product += exp_spectrum[index].getIntensity() * theo_intensity; // fragment annotations in XL-MS data are more complex and do not start with the ion type, but the ion type always follows after a $ if ((*ion_names)[i][0] == 'y' || (*ion_names)[i].hasSubstring("$y")) { + dot_product += exp_spectrum[index].getIntensity() * theo_intensity; #ifdef DEBUG_HYPERSCORE std::cout << (*ion_names)[i] << " intensity: " << exp_spectrum[index].getIntensity() << std::endl; #endif @@ -193,6 +194,8 @@ namespace OpenMS } else if ((*ion_names)[i][0] == 'b' || (*ion_names)[i].hasSubstring("$b")) { + dot_product += exp_spectrum[index].getIntensity() * theo_intensity; + #ifdef DEBUG_HYPERSCORE std::cout << (*ion_names)[i] << " intensity: " << exp_spectrum[index].getIntensity() << std::endl; #endif @@ -201,6 +204,140 @@ namespace OpenMS } } + if (y_ion_count == 0 && b_ion_count == 0) return 0; + + const double yFact = logfactorial_(y_ion_count); + const double bFact = logfactorial_(b_ion_count); + const double hyperScore = log1p(dot_product) + yFact + bFact; + #ifdef DEBUG_HYPERSCORE + std::cout << "HyperScore/#y/#b: " << hyperScore << "/" << y_ion_count << "/" << b_ion_count << std::endl; + #endif + return hyperScore; + } + + + double HyperScore::compute(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const DataArrays::IntegerDataArray& exp_charges, + const PeakSpectrum& theo_spectrum, + const DataArrays::IntegerDataArray& theo_charges, + std::vector& intensity_sum) + { + if (exp_spectrum.size() < 1 || theo_spectrum.size() < 1) + { + std::cout << "Warning: HyperScore: One of the given spectra is empty." << std::endl; + return 0.0; + } + + // TODO this assumes only one StringDataArray is present and it is the right one + const PeakSpectrum::StringDataArray* ion_names; + if (theo_spectrum.getStringDataArrays().size() > 0) + { + ion_names = &theo_spectrum.getStringDataArrays()[0]; + } + else + { + std::cout << "Error: HyperScore: Theoretical spectrum without StringDataArray (\"IonNames\" annotation) provided." << std::endl; + return 0.0; + } + + if (theo_charges.size() != theo_spectrum.size()) + { + std::cout << "Error: HyperScore: #charges != #peaks in theoretical spectrum." << std::endl; + return 0.0; + } + + if (exp_charges.size() != exp_spectrum.size()) + { + std::cout << "Error: HyperScore: #charges != #peaks in experimental spectrum." << std::endl; + return 0.0; + } + + double dot_product = 0.0; + const Size N = intensity_sum.size(); // length of peptide + std::vector b_ions(N, 0.0); + std::vector y_ions(N, 0.0); + + for (Size i = 0; i < theo_spectrum.size(); ++i) + { + const double theo_mz = theo_spectrum[i].getMZ(); + + double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + + // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak + Size index = exp_spectrum.findNearest(theo_mz); + + const double exp_mz = exp_spectrum[index].getMZ(); + const double theo_intensity = theo_spectrum[i].getIntensity(); + const int exp_z = exp_charges[index]; + const int theo_z = theo_charges[i]; + + #ifdef DEBUG_HYPERSCORE + if (exp_z != theo_z) std::cout << "exp_z != theo_z " << exp_z << "\t" << theo_z << std::endl; + #endif + + // found peak match + if (std::abs(theo_mz - exp_mz) < max_dist_dalton + && exp_z == theo_z) + { + // fragment annotations in XL-MS data are more complex and do not start with the ion type, but the ion type always follows after a $ + if ((*ion_names)[i][0] == 'y') + { + auto start = (*ion_names)[i].begin() + 1; + auto end = (*ion_names)[i].end(); + int ii(0); + if (!StringUtils::extractInt(start, end, ii)) continue; + dot_product += exp_spectrum[index].getIntensity() * theo_intensity; + + + #ifdef DEBUG_HYPERSCORE + std::cout << (*ion_names)[i] << " intensity: " << exp_spectrum[index].getIntensity() << std::endl; + std::cout << "N:" << N << "\t" << ii << "\t" << N-1 - (ii-1) << std::endl; + #endif + // we observed the suffix (N-1-ii, N-1] in 0-based AA coordinates + y_ions[N-1 - (ii-1)] += exp_spectrum[index].getIntensity(); + } + else if ((*ion_names)[i][0] == 'b') + { + auto start = (*ion_names)[i].begin() + 1; + auto end = (*ion_names)[i].end(); + int ii(0); + if (!StringUtils::extractInt(start, end, ii)) continue; + dot_product += exp_spectrum[index].getIntensity() * theo_intensity; + + #ifdef DEBUG_HYPERSCORE + std::cout << (*ion_names)[i] << " intensity: " << exp_spectrum[index].getIntensity() << std::endl; + std::cout << "N:" << N << "\t" << ii << "\t" << (ii-1) << std::endl; + #endif + // we observed the prefix [0, ii) in 0-based AA coordinates + b_ions[ii - 1] += exp_spectrum[index].getIntensity(); + } + } + } + + UInt y_ion_count(0), + b_ion_count(0); + for (Size i = 0; i != b_ions.size(); ++i) + { + if (b_ions[i] > 0) + { + ++b_ion_count; + intensity_sum[i] += b_ions[i]; + } + } + + for (Size i = 0; i != y_ions.size(); ++i) + { + if (y_ions[i] > 0) + { + ++y_ion_count; + intensity_sum[i] += y_ions[i]; + } + } + + if (y_ion_count == 0 && b_ion_count == 0) return 0; + const double yFact = logfactorial_(y_ion_count); const double bFact = logfactorial_(b_ion_count); const double hyperScore = log1p(dot_product) + yFact + bFact; @@ -210,5 +347,6 @@ namespace OpenMS return hyperScore; } + } diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 322df8f0039..5f351845275 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -94,12 +94,224 @@ #define NUMBER_OF_THREADS (1) #endif -//#define DEBUG_RNPXLSEARCH +//#define DEBUG_RNPXLSEARCH 1 using namespace OpenMS; using namespace OpenMS::Internal; using namespace std; + // stores which residues (known to give rise to immonium ions) are in the sequence +struct ImmoniumIonsInPeptide +{ + ImmoniumIonsInPeptide(const String& s) + { + for (const char & c : s) + { + switch(c) + { + case 'Y': Y = true; break; + case 'W': W = true; break; + case 'F': F = true; break; + case 'H': H = true; break; + case 'C': C = true; break; + case 'P': P = true; break; + case 'I': + case 'L': L = true; break; + case 'K': K = true; break; + case 'M': M = true; break; + default: break; + } + } + } + bool Y = false; + bool W = false; + bool F = false; + bool H = false; + bool C = false; + bool P = false; + bool L = false; + bool K = false; + bool M = false; +}; + +struct RNPxlFragmentAdductDefinition +{ + EmpiricalFormula formula; // formula + String name; // name used in annotation + double mass = 0; + + RNPxlFragmentAdductDefinition() = default; + + RNPxlFragmentAdductDefinition(const RNPxlFragmentAdductDefinition&) = default; + + RNPxlFragmentAdductDefinition(RNPxlFragmentAdductDefinition&&) = default; + + RNPxlFragmentAdductDefinition& operator=(const RNPxlFragmentAdductDefinition&) = default; + + RNPxlFragmentAdductDefinition& operator=(RNPxlFragmentAdductDefinition&&) = default; + + bool operator<(const RNPxlFragmentAdductDefinition& other) const + { + String fa = formula.toString(); + String fb = other.formula.toString(); + return std::tie(mass, fa, name) < std::tie(other.mass, fb, other.name); + } + + bool operator==(const RNPxlFragmentAdductDefinition& other) const + { + return std::tie(formula, name) == std::tie(other.formula, other.name); + } + +}; + +// fast (flat) data structure to store feasible x-,y-,a-ion fragment adducts and observable marker ions +using NucleotideToFeasibleFragmentAdducts = pair >; + +// stores the fragment adducts and marker ions for a given precursor adduct +struct MS2AdductsOfSinglePrecursorAdduct +{ + vector feasible_adducts; + vector marker_ions; +}; + +// helper struct to facilitate parsing of parameters (modifications, nucleotide adducts, ...) +struct RNPxlParameterParsing +{ + /// Query ResidueModifications (given as strings) from ModificationsDB + static vector getModifications(StringList modNames); + + // Map a nucleotide (e.g. U to all possible fragment adducts) + using NucleotideToFragmentAdductMap = map >; + // @brief Parse tool parameter to create map from target nucleotide to all its fragment adducts + // It maps a single letter nucleotide (e.g., 'T', 'C', ...) + // to the maximum set of fragment adducts that may arise if the nucleotide is cross-linked. + // Losses, that might reduce this set, are not considered in this data structure and handled later + // when specific precursor adducts are considered. + static NucleotideToFragmentAdductMap getTargetNucleotideToFragmentAdducts(StringList fragment_adducts); + + // @brief Determines the fragment adducts and marker ions for a given precursor. + // The precursor adduct (the oligo including losses, e.g.: "TC-H3PO4") is mapped to all contained nucleotides + // and their marker ions. In addition, each cross-linkable nucleotide is mapped to its chemically feasible fragment adducts. + // Chemical feasible means in this context, that the fragment or marker ion adduct is a subformula of the precursor adduct. + static MS2AdductsOfSinglePrecursorAdduct getFeasibleFragmentAdducts( + const String& exp_pc_adduct, + const String& exp_pc_formula, + const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, + const set& can_xl + ); + + // Maps a precursor adduct (e.g.: "UU-H2O") to all chemically feasible fragment adducts. + using PrecursorsToMS2Adducts = map; + + // @brief Calculate all chemically feasible fragment adducts for all possible precursor adducts + // Same as getFeasibleFragmentAdducts but calculated from all precursor adducts + static PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts( + const RNPxlModificationMassesResult& precursor_adducts, + const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, + const set& can_xl); +}; + +/// Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space +/// floats need to be initialized to zero as default +class AnnotatedHit +{ + public: + StringView sequence; + SignedSize peptide_mod_index = 0; // enumeration index of the non-RNA peptide modification + Size rna_mod_index = 0; // index of the RNA modification + int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment + + float mass_error_p = 0; + + static constexpr const char UNKNOWN_NUCLEOTIDE = '?'; + char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE; + // main score + float score = 0; + + float total_loss_score = 0; + // total loss morpheus related subscores + float MIC = 0; + float err = 0; + float Morph = 0; + + float modds = 0; // match odds + + // partial loss morpheus related subscores + float pl_MIC = 0; + float pl_err = 0; + float pl_Morph = 0; + float pl_modds = 0; // match odds + float pl_pc_MIC = 0; + float pl_im_MIC = 0; + + // complete TIC fraction of explained peaks + float total_MIC = 0; + + // subscores + float partial_loss_score = 0; + float immonium_score = 0; + float precursor_score = 0; + float a_ion_score = 0; + float marker_ions_score = 0; + + float best_localization_score = 0; + String localization_scores; + String best_localization; + std::vector fragment_annotations; + + static bool hasBetterScore(const AnnotatedHit& a, const AnnotatedHit& b) + { + return a.score > b.score; + } +}; + +// helper class that adds special ions not covered by TheoreticalSpectrumGenerator +class RNPxlFragmentIonGenerator +{ + public: + // prefix used to denote marker ions in fragment annotations + static constexpr const char* ANNOTATIONS_MARKER_ION_PREFIX = "MI:"; + + // add RNA-marker ions of charge 1 + // this includes the protonated nitrogenous base and all shifts (e.g., U-H2O, U'-H20, ...) + static void addMS2MarkerIons( + const vector& marker_ions, + PeakSpectrum& spectrum, + PeakSpectrum::IntegerDataArray& spectrum_charge, + PeakSpectrum::StringDataArray& spectrum_annotation); + + static void addShiftedImmoniumIons( + const String & unmodified_sequence, + const String & fragment_shift_name, + const double fragment_shift_mass, + PeakSpectrum & partial_loss_spectrum, + PeakSpectrum::IntegerDataArray& partial_loss_spectrum_charge, + PeakSpectrum::StringDataArray& partial_loss_spectrum_annotation); + + static void generatePartialLossSpectrum(const String& unmodified_sequence, + const double& fixed_and_variable_modified_peptide_weight, + const String& precursor_rna_adduct, + const double& precursor_rna_mass, + const int& precursor_charge, + const vector& partial_loss_modification, + const PeakSpectrum& patial_loss_template_z1, + const PeakSpectrum& patial_loss_template_z2, + const PeakSpectrum& patial_loss_template_z3, + PeakSpectrum& partial_loss_spectrum); + static void addPrecursorWithCompleteRNA_(const double fixed_and_variable_modified_peptide_weight, + const String & precursor_rna_adduct, + const double precursor_rna_mass, + const int charge, + PeakSpectrum & partial_loss_spectrum, + MSSpectrum::IntegerDataArray & partial_loss_spectrum_charge, + MSSpectrum::StringDataArray & partial_loss_spectrum_annotation); + + static void addSpecialLysImmonumIons(const String& unmodified_sequence, + PeakSpectrum &spectrum, + PeakSpectrum::IntegerDataArray &spectrum_charge, + PeakSpectrum::StringDataArray &spectrum_annotation); +}; + class RNPxlSearch : public TOPPBase { @@ -120,6 +332,7 @@ class RNPxlSearch : static constexpr double MIN_TOTAL_LOSS_IONS = 1; // minimum number of matches to unshifted ions static constexpr double MIN_SHIFTED_IONS = 1; // minimum number of matches to shifted ions (applies to XLs only) protected: + void registerOptionsAndFlags_() override { registerInputFile_("in", "", "", "input file "); @@ -252,136 +465,314 @@ class RNPxlSearch : registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); } - struct FragmentAdductDefinition_ - { - EmpiricalFormula formula; // formula - String name; // name used in annotation - double mass = 0; + static double matchOddsScore_( + const Size& N, + const Size matched_size) + { + if (matched_size < 1 || N < 1) { return 0; } - FragmentAdductDefinition_() = default; + const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see ThresholdMower) + const double pscore = boost::math::ibeta(matched_size + 1, N - matched_size, p); + if (pscore <= std::numeric_limits::min()) return -log10(std::numeric_limits::min()); + const double minusLog10p1pscore = -log10(pscore); + return minusLog10p1pscore; + } - FragmentAdductDefinition_(const FragmentAdductDefinition_&) = default; + static void generateTheoreticalMZsZ1_(const AASequence& peptide, + const Residue::ResidueType& res_type, + std::vector& mzs) + { + const Size N = peptide.size(); + mzs.resize(N-1); + double mono_weight(Constants::PROTON_MASS_U); + if (res_type == Residue::BIon || res_type == Residue::AIon || res_type == Residue::CIon) + { + if (peptide.hasNTerminalModification()) + { + mono_weight += peptide.getNTerminalModification()->getDiffMonoMass(); + } - FragmentAdductDefinition_(FragmentAdductDefinition_&&) = default; + switch (res_type) + { + case Residue::AIon: mono_weight += Residue::getInternalToAIon().getMonoWeight(); break; + case Residue::BIon: mono_weight += Residue::getInternalToBIon().getMonoWeight(); break; + case Residue::CIon: mono_weight += Residue::getInternalToCIon().getMonoWeight(); break; + default: break; + } - FragmentAdductDefinition_& operator=(const FragmentAdductDefinition_&) = default; + for (Size i = 0; i < N-1; ++i) // < N-1: don't add last residue as it is part of precursor + { + mono_weight += peptide[i].getMonoWeight(Residue::Internal); + mzs[i] = mono_weight; + } + } + else // if (res_type == Residue::XIon || res_type == Residue::YIon || res_type == Residue::ZIon) + { + if (peptide.hasCTerminalModification()) + { + mono_weight += peptide.getCTerminalModification()->getDiffMonoMass(); + } - FragmentAdductDefinition_& operator=(FragmentAdductDefinition_&&) = default; + switch (res_type) + { + case Residue::XIon: mono_weight += Residue::getInternalToXIon().getMonoWeight(); break; + case Residue::YIon: mono_weight += Residue::getInternalToYIon().getMonoWeight(); break; + case Residue::ZIon: mono_weight += Residue::getInternalToZIon().getMonoWeight(); break; + default: break; + } - bool operator<(const FragmentAdductDefinition_& other) const - { - String fa = formula.toString(); - String fb = other.formula.toString(); - return std::tie(mass, fa, name) < std::tie(other.mass, fb, other.name); + for (Size i = N-1; i > 0; --i) // > 0: don't add last residue (part of precursor ion) + { + mono_weight += peptide[i].getMonoWeight(Residue::Internal); + mzs[N-1-i] = mono_weight; + } + } + } + + static double logfactorial_(UInt x) + { + if (x < 2) { return 0; } + double z(0); + for (double y = 2; y <= static_cast(x); ++y) { z += log(static_cast(y)); } + return z; } - bool operator==(const FragmentAdductDefinition_& other) const + + static void scoreShiftedLadderIons_( + const vector& partial_loss_modification, + const vector& partial_loss_template_z1_b_ions, + const vector& partial_loss_template_z1_y_ions, + const double peptide_mass_without_NA, + const unsigned int pc_charge, + const ImmoniumIonsInPeptide& iip, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const DataArrays::IntegerDataArray& exp_charges, + std::vector& intensity_sum, + float& plss_hyperScore, + float& plss_MIC, + float& plss_Morph, + float& plss_err, + float& plss_pc_MIC, + float& plss_im_MIC) + { + OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); + OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); + OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); + OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_y_ions.size(), "Sum array needs to be of same size as y-ion array"); + OPENMS_PRECONDITION(partial_loss_template_z1_b_ions.size() == partial_loss_template_z1_y_ions.size(), "b- and y-ion arrays must have same size."); + OPENMS_PRECONDITION(partial_loss_template_z1_b_ions.size() > 0, "b- and y-ion arrays must not be empty."); + + double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); + const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 + std::vector b_ions(N, 0.0), y_ions(N, 0.0); + + // maximum charge considered + const Size max_z = std::min(pc_charge - 1, 2U); + + // match b- and a-ions (we record a-ions as b-ions) + for (double diff2b : {0.0, -27.994915} ) // b-ion and a-ion ('CO' mass diff from b- to a-ion) + { + for (Size z = 1; z <= max_z; ++z) + { + for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) + { + for (Size i = 0; i < partial_loss_template_z1_b_ions.size(); ++i) + { + const double theo_mz = (partial_loss_template_z1_b_ions[i] + fa.mass + diff2b + + (z-1) * Constants::PROTON_MASS_U) / z; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + + // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak + Size index = exp_spectrum.findNearest(theo_mz); + + const double exp_mz = exp_spectrum[index].getMZ(); + const int exp_z = exp_charges[index]; + + // found peak match + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + const double intensity = exp_spectrum[index].getIntensity(); + b_mean_err += intensity * std::abs(theo_mz - exp_mz); + dot_product += intensity ; + b_ions[i] += intensity ; + } + } + } + } + } + + // match y-ions + for (Size z = 1; z <= max_z; ++z) { - return std::tie(formula, name) == std::tie(other.formula, other.name); + for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) + { + for (int i = 0; i < partial_loss_template_z1_y_ions.size(); ++i) + { + const double theo_mz = (partial_loss_template_z1_y_ions[i] + fa.mass + + (z-1) * Constants::PROTON_MASS_U) / z; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + + // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak + Size index = exp_spectrum.findNearest(theo_mz); + + const double exp_mz = exp_spectrum[index].getMZ(); + const int exp_z = exp_charges[index]; + + // found peak match + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + const double intensity = exp_spectrum[index].getIntensity(); + y_mean_err += intensity * std::abs(theo_mz - exp_mz); + dot_product += intensity; + y_ions[N-1 - i] += intensity; + } + } + } } - }; + UInt y_ion_count(0), b_ion_count(0); + double b_sum(0.0); + for (Size i = 0; i != b_ions.size(); ++i) + { + if (b_ions[i] > 0) + { + intensity_sum[i] += b_ions[i]; + b_sum += b_ions[i]; + ++b_ion_count; + } + } - // fast (flat) data structure to store feasible x-,y-,a-ion fragment adducts and observable marker ions - using NucleotideToFeasibleFragmentAdducts = pair >; + double y_sum(0.0); + for (Size i = 0; i != y_ions.size(); ++i) + { + if (y_ions[i] > 0) + { + intensity_sum[i] += y_ions[i]; + y_sum += y_ions[i]; + ++y_ion_count; + } + } - // stores the fragment adducts and marker ions for a given precursor adduct - struct MS2AdductsOfSinglePrecursorAdduct - { - vector feasible_adducts; - vector marker_ions; - }; + // TODO: calculate this once and store in exp_spectrum meta data? + double TIC = std::accumulate(exp_spectrum.begin(), exp_spectrum.end(), 0.0, + [&](double a, const Peak1D& b) { return a + b.getIntensity(); }); - // helper struct to facilitate parsing of parameters (modifications, nucleotide adducts, ...) - struct RNPxlParameterParsing - { - /// Query ResidueModifications (given as strings) from ModificationsDB - static vector getModifications(StringList modNames); - - // Map a nucleotide (e.g. U to all possible fragment adducts) - using NucleotideToFragmentAdductMap = map >; - // @brief Parse tool parameter to create map from target nucleotide to all its fragment adducts - // It maps a single letter nucleotide (e.g., 'T', 'C', ...) - // to the maximum set of fragment adducts that may arise if the nucleotide is cross-linked. - // Losses, that might reduce this set, are not considered in this data structure and handled later - // when specific precursor adducts are considered. - static NucleotideToFragmentAdductMap getTargetNucleotideToFragmentAdducts(StringList fragment_adducts); - - - // @brief Determines the fragment adducts and marker ions for a given precursor. - // The precursor adduct (the oligo including losses, e.g.: "TC-H3PO4") is mapped to all contained nucleotides - // and their marker ions. In addition, each cross-linkable nucleotide is mapped to its chemically feasible fragment adducts. - // Chemical feasible means in this context, that the fragment or marker ion adduct is a subformula of the precursor adduct. - static MS2AdductsOfSinglePrecursorAdduct getFeasibleFragmentAdducts( - const String& exp_pc_adduct, - const String& exp_pc_formula, - const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, - const set& can_xl - ); + if (y_ion_count == 0 && b_ion_count == 0) + { + plss_hyperScore = 0; + plss_MIC = 0; + plss_Morph = 0; + plss_err = fragment_mass_tolerance_unit_ppm ? 2000.0 * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance;; + } + else + { + const double yFact = logfactorial_(y_ion_count); + const double bFact = logfactorial_(b_ion_count); + plss_hyperScore = log1p(dot_product) + yFact + bFact; + plss_MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); + plss_MIC /= TIC; + plss_Morph = b_ion_count + y_ion_count + plss_MIC; + plss_err = (y_mean_err + b_mean_err)/(b_sum + y_sum); + } + + // match (partially) shifted precusor ions z = 1..pc_charge + for (double pc_loss : {0.0, -18.010565, -17.026548} ) // normal, loss of water, loss of ammonia + { + const double peptide_mass = peptide_mass_without_NA + pc_loss; + for (Size z = 1; z <= pc_charge; ++z) + { + for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) + { + const double theo_mz = (peptide_mass + fa.mass + z * Constants::PROTON_MASS_U) / z; - // Maps a precursor adduct (e.g.: "UU-H2O") to all chemically feasible fragment adducts. - using PrecursorsToMS2Adducts = map; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + Size index = exp_spectrum.findNearest(theo_mz); + const double exp_mz = exp_spectrum[index].getMZ(); + const int exp_z = exp_charges[index]; - // @brief Calculate all chemically feasible fragment adducts for all possible precursor adducts - // Same as getFeasibleFragmentAdducts but calculated from all precursor adducts - static PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts( - const RNPxlModificationMassesResult& precursor_adducts, - const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, - const set& can_xl); + // found peak match + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + const double intensity = exp_spectrum[index].getIntensity(); + plss_pc_MIC += intensity; + } + } + } + } + plss_pc_MIC /= TIC; - }; + // shifted immonium ions - /// Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space - /// floats need to be initialized to zero as default - class AnnotatedHit - { - public: - StringView sequence; - SignedSize peptide_mod_index = 0; // enumeration index of the non-RNA peptide modification - Size rna_mod_index = 0; // index of the RNA modification - int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment - - float mass_error_p = 0; - - static constexpr const char UNKNOWN_NUCLEOTIDE = '?'; - char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE; - // main score - float score = 0; - - float total_loss_score = 0; - // total loss morpheus related subscores - float MIC = 0; - float err = 0; - float Morph = 0; - - float modds = 0; // match odds - - // partial loss morpheus related subscores - float pl_MIC = 0; - float pl_err = 0; - float pl_Morph = 0; - float pl_modds = 0; // match odds - - // complete TIC fraction of explained peaks - float total_MIC = 0; - - // subscores - float partial_loss_score = 0; - float immonium_score = 0; - float precursor_score = 0; - float a_ion_score = 0; - float marker_ions_score = 0; - - float best_localization_score = 0; - String localization_scores; - String best_localization; - std::vector fragment_annotations; - - static bool hasBetterScore(const AnnotatedHit& a, const AnnotatedHit& b) + // lambda to match one peak and sum up in score + auto match_one_peak_z1 = [&](const double& theo_mz, float& score) + { + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + auto index = exp_spectrum.findNearest(theo_mz); + if (exp_charges[index] == 1 && + std::abs(theo_mz - exp_spectrum[index].getMZ()) < max_dist_dalton) // found peak match + { + score += exp_spectrum[index].getIntensity(); + } + }; + + static const double imY = EmpiricalFormula("C8H10NO").getMonoWeight(); + static const double imW = EmpiricalFormula("C10H11N2").getMonoWeight(); + static const double imF = EmpiricalFormula("C8H10N").getMonoWeight(); + static const double imH = EmpiricalFormula("C5H8N3").getMonoWeight(); + static const double imC = EmpiricalFormula("C2H6NS").getMonoWeight(); + static const double imP = EmpiricalFormula("C4H8N").getMonoWeight(); + static const double imL = EmpiricalFormula("C5H12N").getMonoWeight(); + static const double imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); + static const double imK2 = EmpiricalFormula("C5H10N1").getMonoWeight(); + static const double imK3 = EmpiricalFormula("C6H13N2O").getMonoWeight(); + + for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { - return a.score > b.score; + if (iip.Y) + { + match_one_peak_z1(imY + fa.mass, plss_im_MIC); + } + if (iip.W) + { + match_one_peak_z1(imW + fa.mass, plss_im_MIC); + } + if (iip.F) + { + match_one_peak_z1(imF + fa.mass, plss_im_MIC); + } + if (iip.H) + { + match_one_peak_z1(imH + fa.mass, plss_im_MIC); + } + if (iip.C) + { + match_one_peak_z1(imC + fa.mass, plss_im_MIC); + } + if (iip.P) + { + match_one_peak_z1(imP + fa.mass, plss_im_MIC); + } + if (iip.L) + { + match_one_peak_z1(imL + fa.mass, plss_im_MIC); + } + if (iip.K) + { + match_one_peak_z1(imK1 + fa.mass, plss_im_MIC); + // according to A. Stuetzer mainly observed with C‘-NH3 (94.0167 Da) + match_one_peak_z1(imK2 + fa.mass, plss_im_MIC); + // usually only observed without shift (A. Stuetzer) + match_one_peak_z1(imK3 + fa.mass, plss_im_MIC); + } + if (iip.M) + { + match_one_peak_z1(104.05285 + fa.mass, plss_im_MIC); + } } - }; + plss_im_MIC /= TIC; + } static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) { @@ -425,8 +816,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 + 0.25318342707227187 * ah.total_loss_score + 0.12472562244230834 * ah.partial_loss_score + 1.2107674392113372 * ah.mass_error_p - + 2.3319284783288805 * ah.pl_MIC - - 0.1821314450150078 * ah.pl_Morph; + + 2.3319284783288805 * ah.pl_MIC; } // return ah.total_loss_score + ah.total_MIC + ah.mass_error_p / 3.0; /* @@ -462,7 +852,85 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 */ } +/* +* Score fragments carrying NA adducts . +*/ +static void scoreShiftedFragments_( + const vector &partial_loss_modification, + const Size peptide_size, + const ImmoniumIonsInPeptide& iip, + const PeakSpectrum &exp_spectrum, + const double peptide_mass_without_NA, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const vector &partial_loss_template_z1_b_ions, + const vector &partial_loss_template_z1_y_ions, + const PeakSpectrum &marker_ions_sub_score_spectrum_z1, + float &partial_loss_sub_score, + float &marker_ions_sub_score, + float &plss_MIC, + float &plss_err, + float &plss_Morph, + float &plss_modds, + float &plss_pc_MIC, + float &plss_im_MIC) + { + const SignedSize& exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); + //const double exp_pc_mz = exp_spectrum.getPrecursors()[0].getMZ(); + + if (!marker_ions_sub_score_spectrum_z1.empty()) + { + auto const & r = MorpheusScore::compute(fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + marker_ions_sub_score_spectrum_z1, + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0]); + marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; + } + //TODO: these are currently empty +/* + if (!shifted_immonium_ions_sub_score_spectrum.empty()) + { + shifted_immonium_ions_sub_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, shifted_immonium_ions_sub_score_spectrum); + shifted_immonium_ions_sub_score(0), + } +*/ + if (!partial_loss_template_z1_b_ions.empty()) // check if we generated partial loss spectra + { + vector intensity_sum(peptide_size - 1, 0.0); + + scoreShiftedLadderIons_( + partial_loss_modification, + partial_loss_template_z1_b_ions, + partial_loss_template_z1_y_ions, + peptide_mass_without_NA, + exp_pc_charge, + iip, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + intensity_sum, + partial_loss_sub_score, + plss_MIC, + plss_Morph, + plss_err, + plss_pc_MIC, + plss_im_MIC); + // if we only have 1 peak assume some kind of average error to not underestimate the real error to much + plss_err = plss_Morph > 2 ? plss_err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; + plss_modds = matchOddsScore_(partial_loss_template_z1_b_ions.size() + + partial_loss_template_z1_y_ions.size(), (int)plss_Morph); + } +#ifdef DEBUG_RNPXLSEARCH + LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; +#endif + // cap plss_err to something larger than the mean_mz * max_ppm_error + float ft_da = fragment_mass_tolerance_unit_ppm ? fragment_mass_tolerance * 1e-6 * 1000.0 : fragment_mass_tolerance; + if (plss_err > ft_da) plss_err = ft_da; + } /* @brief Filter spectra to remove noise. Parameter are passed to spectra filter. @@ -568,54 +1036,6 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 } } - // prefix used to denote marker ions in fragment annotations - static constexpr const char* ANNOTATIONS_MARKER_ION_PREFIX = "MI:"; - - // helper class that adds special ions not covered by TheoreticalSpectrumGenerator - class RNPxlFragmentIonGenerator - { - public: - // add RNA-marker ions of charge 1 - // this includes the protonated nitrogenous base and all shifts (e.g., U-H2O, U'-H20, ...) - static void addMS2MarkerIons( - const vector& marker_ions, - PeakSpectrum& spectrum, - PeakSpectrum::IntegerDataArray& spectrum_charge, - PeakSpectrum::StringDataArray& spectrum_annotation); - - static void addShiftedImmoniumIons( - const String & unmodified_sequence, - const String & fragment_shift_name, - const double fragment_shift_mass, - PeakSpectrum & partial_loss_spectrum, - PeakSpectrum::IntegerDataArray& partial_loss_spectrum_charge, - PeakSpectrum::StringDataArray& partial_loss_spectrum_annotation); - - static void generatePartialLossSpectrum(const String& unmodified_sequence, - const double& fixed_and_variable_modified_peptide_weight, - const String& precursor_rna_adduct, - const double& precursor_rna_mass, - const int& precursor_charge, - const vector& partial_loss_modification, - const PeakSpectrum& patial_loss_template_z1, - const PeakSpectrum& patial_loss_template_z2, - const PeakSpectrum& patial_loss_template_z3, - PeakSpectrum& partial_loss_spectrum); - static void addPrecursorWithCompleteRNA_(const double fixed_and_variable_modified_peptide_weight, - const String & precursor_rna_adduct, - const double precursor_rna_mass, - const int charge, - PeakSpectrum & partial_loss_spectrum, - MSSpectrum::IntegerDataArray & partial_loss_spectrum_charge, - MSSpectrum::StringDataArray & partial_loss_spectrum_annotation); - - static void addSpecialLysImmonumIons(const String& unmodified_sequence, - PeakSpectrum &spectrum, - PeakSpectrum::IntegerDataArray &spectrum_charge, - PeakSpectrum::StringDataArray &spectrum_annotation); - }; - - /* @brief Localization step of the cross-link identification engine. * Given a top scoring candidate (based on total loss spectrum) it: * - generates all fragment adducts based on the attached precursor adduct @@ -715,7 +1135,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 std::advance(mod_combinations_it, ah.rna_mod_index); const String precursor_rna_adduct = *mod_combinations_it->second.begin(); const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; - const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; + const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); if (precursor_rna_adduct == "none") @@ -725,7 +1145,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 } // determine current nucleotide and associated partial losses - vector partial_loss_modification; + vector partial_loss_modification; for (auto const & nuc_2_adducts : feasible_MS2_adducts) { if(nuc_2_adducts.first == ah.cross_linked_nucleotide) @@ -764,7 +1184,6 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 partial_loss_template_z2, partial_loss_template_z3, partial_loss_spectrum_z1); - for (auto& n : partial_loss_spectrum_z1.getStringDataArrays()[0]) { n[0] = 'y'; } // hyperscore hack RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, current_peptide_mass_without_RNA, @@ -776,7 +1195,6 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 partial_loss_template_z2, partial_loss_template_z3, partial_loss_spectrum_z2); - for (auto& n : partial_loss_spectrum_z2.getStringDataArrays()[0]) { n[0] = 'y'; } // hyperscore hack } // add shifted marker ions @@ -794,10 +1212,10 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 plss_MIC(0), plss_err(1.0), plss_Morph(0), - plss_modds(0), - tlss_score(0); + plss_modds(0); - scorePartialLossFragments_(exp_spectrum, + scorePartialLossFragments_( unmodified_sequence.size(), + exp_spectrum, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, partial_loss_spectrum_z1, @@ -882,10 +1300,10 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 OPENMS_POSTCONDITION(nt_to_adducts != feasible_MS2_adducts.end(), "Nucleotide not found in mapping to feasible adducts.") - const vector& partial_loss_modification = nt_to_adducts->second; + const vector& partial_loss_modification = nt_to_adducts->second; // get marker ions (these are not specific to the cross-linked nucleotide but also depend on the whole oligo bound to the precursor) - const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; + const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; // generate total loss spectrum for the fixed and variable modified peptide (without RNA) (using the settings for partial loss generation) // but as we also add the abundant immonium ions for charge 1 and precursor ions for all charges to get a more complete annotation @@ -944,11 +1362,11 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 // ion centric (e.g. b and y-ion) spectrum annotation that records all shifts of specific ions (e.g. y5, y5 + U, y5 + C3O) using MapIonIndexToFragmentAnnotation = map >; MapIonIndexToFragmentAnnotation unshifted_b_ions, unshifted_y_ions, unshifted_a_ions, shifted_b_ions, shifted_y_ions, shifted_a_ions; - vector shifted_immonium_ions; - vector unshifted_loss_ions; - vector annotated_marker_ions; - vector annotated_precursor_ions; - vector annotated_immonium_ions; + vector shifted_immonium_ions, + unshifted_loss_ions, + annotated_marker_ions, + annotated_precursor_ions, + annotated_immonium_ions; // first annotate total loss peaks (these give no information where the actual shift occured) #ifdef DEBUG_RNPXLSEARCH @@ -1204,7 +1622,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); shifted_a_ions[ion_number].push_back(d); } - else if (ion_name.hasPrefix(ANNOTATIONS_MARKER_ION_PREFIX)) + else if (ion_name.hasPrefix(RNPxlFragmentIonGenerator::ANNOTATIONS_MARKER_ION_PREFIX)) { if (fragment_charge == 1) { @@ -1525,6 +1943,9 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 ph.setMetaValue(String("RNPxl:pl_err"), ah.pl_err); ph.setMetaValue(String("RNPxl:pl_Morph"), ah.pl_Morph); ph.setMetaValue(String("RNPxl:pl_modds"), ah.pl_modds); + ph.setMetaValue(String("RNPxl:pl_pc_MIC"), ah.pl_pc_MIC); + ph.setMetaValue(String("RNPxl:pl_im_MIC"), ah.pl_im_MIC); + ph.setMetaValue(String("RNPxl:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses ph.setMetaValue(String("RNPxl:RNA"), *mod_combinations_it->second.begin()); // return first nucleotide formula matching the index of the empirical formula @@ -1604,6 +2025,8 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 << "RNPxl:pl_err" << "RNPxl:pl_Morph" << "RNPxl:pl_modds" + << "RNPxl:pl_pc_MIC" + << "RNPxl:pl_im_MIC" << "RNPxl:total_MIC" << "RNPxl:RNA_MASS_z0" << "precursor_intensity_log10"; @@ -2027,6 +2450,9 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 const String unmodified_sequence = cit->getString(); + // determine which residues might give rise to an immonium ion + ImmoniumIonsInPeptide iip(unmodified_sequence); + #ifdef _OPENMP #pragma omp critical (residuedb_access) #endif @@ -2151,7 +2577,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 // bad score or less then two peaks matching if (total_loss_score < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_modds < 1e-10 + || tlss_modds < 1e-10 || tlss_MIC < 0.01) { continue; @@ -2206,17 +2632,12 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 } else // score peptide with RNA adduct { - PeakSpectrum partial_loss_template_z1, partial_loss_template_z2, partial_loss_template_z3; - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); - // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum // get RNA fragment shifts in the MS2 (based on the precursor RNA/DNA) auto const & all_NA_adducts = all_feasible_fragment_adducts.at(precursor_rna_adduct); const vector& feasible_MS2_adducts = all_NA_adducts.feasible_adducts; // get marker ions - const vector& marker_ions = all_NA_adducts.marker_ions; + const vector& marker_ions = all_NA_adducts.marker_ions; //cout << "'" << precursor_rna_adduct << "'" << endl; //OPENMS_POSTCONDITION(!feasible_MS2_adducts.empty(), @@ -2232,9 +2653,11 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 { // determine current nucleotide and associated partial losses const char& cross_linked_nucleotide = nuc_2_adducts.first; - const vector& partial_loss_modification = nuc_2_adducts.second; + const vector& partial_loss_modification = nuc_2_adducts.second; + - PeakSpectrum marker_ions_sub_score_spectrum_z1, + PeakSpectrum marker_ions_sub_score_spectrum_z1; + /*, partial_loss_spectrum_z1, partial_loss_spectrum_z2; @@ -2242,7 +2665,6 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 if (!partial_loss_modification.empty()) { // shifted b- / y- / a-ions - // generate shifted_immonium_ions_sub_score_spectrum.empty RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, current_peptide_mass_without_RNA, precursor_rna_adduct, @@ -2253,7 +2675,6 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 partial_loss_template_z2, partial_loss_template_z3, partial_loss_spectrum_z1); - for (auto& n : partial_loss_spectrum_z1.getStringDataArrays()[0]) { n[0] = 'y'; } // hyperscore hack RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, current_peptide_mass_without_RNA, @@ -2265,9 +2686,8 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 partial_loss_template_z2, partial_loss_template_z3, partial_loss_spectrum_z2); - for (auto& n : partial_loss_spectrum_z2.getStringDataArrays()[0]) { n[0] = 'y'; } // hyperscore hack } - +*/ // add shifted marker ions marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation @@ -2277,9 +2697,17 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0], marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); + + // nucleotide is associated with certain NA-related fragment losses? + vector partial_loss_template_z1_bions, partial_loss_template_z1_yions; + if (!partial_loss_modification.empty()) + { + generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::BIon, partial_loss_template_z1_bions); + generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::YIon, partial_loss_template_z1_yions); + } + for (auto l = low_it; l != up_it; ++l) { - //const double exp_pc_mass = l->first; const Size& scan_index = l->second.first; const int& isotope_error = l->second.second; const PeakSpectrum& exp_spectrum = spectra[scan_index]; @@ -2292,10 +2720,6 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 a_ion_sub_score(0), partial_loss_sub_score(0), marker_ions_sub_score(0), - plss_MIC(0), - plss_err(1.0), - plss_Morph(0), - plss_modds(0), tlss_score(0); const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); @@ -2303,7 +2727,8 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 scoreTotalLossFragments_(exp_spectrum, total_loss_spectrum, - fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, a_ion_sub_score_spectrum, precursor_sub_score_spectrum, immonium_sub_score_spectrum, @@ -2325,20 +2750,35 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 continue; } - scorePartialLossFragments_(exp_spectrum, + float plss_MIC(0), + plss_err(1.0), + plss_Morph(0), + plss_modds(0), + plss_pc_MIC(0), + plss_im_MIC(0); + + scoreShiftedFragments_( partial_loss_modification, + unmodified_sequence.size(), + iip, + exp_spectrum, + current_peptide_mass_without_RNA, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - partial_loss_spectrum_z1, - partial_loss_spectrum_z2, + partial_loss_template_z1_bions, + partial_loss_template_z1_yions, marker_ions_sub_score_spectrum_z1, partial_loss_sub_score, marker_ions_sub_score, plss_MIC, plss_err, plss_Morph, - plss_modds); + plss_modds, + plss_pc_MIC, + plss_im_MIC); + + const double total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score + + plss_MIC + plss_pc_MIC + plss_im_MIC; - const double total_MIC = tlss_MIC + plss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; // less then two shifted peaks? seems to throw out some good hits ??? /* if ( partial_loss_sub_score < MIN_HYPERSCORE // at least one peak with 10% of max intensity || plss_Morph < MIN_SHIFTED_IONS + 1.0 // > 1 shifted peaks @@ -2366,6 +2806,8 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 ah.pl_err = plss_err; ah.pl_Morph = plss_Morph; ah.pl_modds = plss_modds; + ah.pl_pc_MIC = plss_pc_MIC; + ah.pl_im_MIC = plss_im_MIC; ah.immonium_score = immonium_sub_score; ah.precursor_score = precursor_sub_score; ah.a_ion_score = a_ion_sub_score; @@ -2630,23 +3072,8 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 return EXECUTION_OK; } - static double matchOddsScore_( - const PeakSpectrum& theoretical_spec, - const Size matched_size) - { - const Size N = theoretical_spec.size(); - - if (matched_size < 1 || N < 1) { return 0; } - - const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see ThresholdMower) - const double pscore = boost::math::ibeta(matched_size + 1, N - matched_size, p); - if (pscore <= std::numeric_limits::min()) return -log10(std::numeric_limits::min()); - const double minusLog10p1pscore = -log10(pscore); - return minusLog10p1pscore; - } - // determine main score and sub scores of peaks without shifts - void scoreTotalLossFragments_(const PeakSpectrum &exp_spectrum, + static void scoreTotalLossFragments_(const PeakSpectrum &exp_spectrum, const PeakSpectrum &total_loss_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, @@ -2660,7 +3087,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 float &tlss_modds, float &immonium_sub_score, float &precursor_sub_score, - float &a_ion_sub_score) const + float &a_ion_sub_score) { total_loss_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, @@ -2693,7 +3120,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 // if we only have 1 or peaks assume some kind of average error to not underestimate the real error to much tlss_err = tlss_Morph > 2 ? tl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - tlss_modds = matchOddsScore_(total_loss_spectrum, (int)tlss_Morph); // (int)Morph == number of matched peaks + tlss_modds = matchOddsScore_(total_loss_spectrum.size(), (int)tlss_Morph); // (int)Morph == number of matched peaks if (!immonium_sub_score_spectrum.empty()) { @@ -2727,7 +3154,8 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 } } - void scorePartialLossFragments_(const PeakSpectrum &exp_spectrum, + static void scorePartialLossFragments_(const Size peptide_size, + const PeakSpectrum &exp_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &partial_loss_spectrum_z1, @@ -2738,7 +3166,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 float &plss_MIC, float &plss_err, float &plss_Morph, - float &plss_modds) const + float &plss_modds) { const SignedSize& exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); @@ -2762,6 +3190,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 */ if (!partial_loss_spectrum_z1.empty()) // check if we generated partial loss spectra { + vector intensity_sum(peptide_size, 0.0); MSSpectrum const * pl_spec = &partial_loss_spectrum_z1; if (exp_pc_charge >= 3) { @@ -2772,7 +3201,9 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 exp_spectrum, exp_spectrum.getIntegerDataArrays()[0], *pl_spec, - pl_spec->getIntegerDataArrays()[0]); + pl_spec->getIntegerDataArrays()[0], + intensity_sum); + auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, @@ -2783,7 +3214,7 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 plss_Morph = pl_sub_scores.score; // if we only have 1 peak assume some kind of average error to not underestimate the real error to much plss_err = plss_Morph > 2 ? pl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - plss_modds = matchOddsScore_(*pl_spec, (int)plss_Morph); + plss_modds = matchOddsScore_(pl_spec->size(), (int)plss_Morph); } #ifdef DEBUG_RNPXLSEARCH LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; @@ -2794,7 +3225,9 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 } }; -vector RNPxlSearch::RNPxlParameterParsing::getModifications(StringList modNames) { + + +vector RNPxlParameterParsing::getModifications(StringList modNames) { vector modifications; // iterate over modification names and add to vector @@ -2821,10 +3254,10 @@ vector RNPxlSearch::RNPxlParameterParsing::getModifications return modifications; } -RNPxlSearch::RNPxlParameterParsing::PrecursorsToMS2Adducts -RNPxlSearch::RNPxlParameterParsing::getAllFeasibleFragmentAdducts( +RNPxlParameterParsing::PrecursorsToMS2Adducts +RNPxlParameterParsing::getAllFeasibleFragmentAdducts( const RNPxlModificationMassesResult &precursor_adducts, - const RNPxlSearch::RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, + const RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, const set &can_xl) { PrecursorsToMS2Adducts all_pc_all_feasible_adducts; @@ -2872,8 +3305,8 @@ RNPxlSearch::RNPxlParameterParsing::getAllFeasibleFragmentAdducts( return all_pc_all_feasible_adducts; } -RNPxlSearch::RNPxlParameterParsing::NucleotideToFragmentAdductMap -RNPxlSearch::RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringList fragment_adducts) +RNPxlParameterParsing::NucleotideToFragmentAdductMap +RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringList fragment_adducts) { NucleotideToFragmentAdductMap nucleotide_to_fragment_adducts; for (String t : fragment_adducts) @@ -2913,7 +3346,7 @@ RNPxlSearch::RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringL return NucleotideToFragmentAdductMap(); } - FragmentAdductDefinition_ fad; + RNPxlFragmentAdductDefinition fad; fad.name = name; fad.formula = formula; fad.mass = formula.getMonoWeight(); @@ -2957,10 +3390,10 @@ RNPxlSearch::RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringL return nucleotide_to_fragment_adducts; } -RNPxlSearch::MS2AdductsOfSinglePrecursorAdduct -RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, +MS2AdductsOfSinglePrecursorAdduct +RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, const String &exp_pc_formula, - const RNPxlSearch::RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, + const RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, const set &can_xl) { LOG_DEBUG << "Generating fragment adducts for precursor adduct: '" << exp_pc_adduct << "'" << endl; @@ -3018,7 +3451,7 @@ RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp for (auto const & n2fa : nucleotide_to_fragment_adducts) { const char & nucleotide = n2fa.first; // the nucleotide without any associated loss - const set& fragment_adducts = n2fa.second; // all potential fragment adducts that may arise from the unmodified nucleotide + const set& fragment_adducts = n2fa.second; // all potential fragment adducts that may arise from the unmodified nucleotide // check if nucleotide is cross-linkable and part of the precursor adduct if (exp_pc_xl_nts.find(nucleotide) != exp_pc_xl_nts.end()) @@ -3027,7 +3460,7 @@ RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp LOG_DEBUG << "\t" << exp_pc_adduct << " nucleotide: " << String(nucleotide) << " has fragment_adducts: " << fragment_adducts.size() << endl; // store feasible adducts associated with a cross-link with character nucleotide - vector faa; + vector faa; std::copy(fragment_adducts.begin(), fragment_adducts.end(), back_inserter(faa)); ret.feasible_adducts.emplace_back(make_pair(nucleotide, faa)); } @@ -3035,7 +3468,7 @@ RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp // Create set of marker ions for all nucleotides contained in the precursor (including those that do not cross-link.) // Note: The non-cross-linked nt in the precursor adduct are more likely to produce the marker ions (=more fragile than the cross-linked nt). - set marker_ion_set; + set marker_ion_set; for (auto const & n2fa : nucleotide_to_fragment_adducts) { const char & nucleotide = n2fa.first; // the nucleotide without any associated loss @@ -3048,7 +3481,7 @@ RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp for (auto const & n2fa : nucleotide_to_fragment_adducts) { const char & nucleotide = n2fa.first; // one letter code of the nt - set fas = n2fa.second; // all potential fragment adducts that may arise from nt (if no losses are considered) + set fas = n2fa.second; // all potential fragment adducts that may arise from nt (if no losses are considered) // check if nucleotide is cross-linkable and part of the precursor adduct if (exp_pc_xl_nts.find(nucleotide) != exp_pc_xl_nts.end()) @@ -3072,7 +3505,7 @@ RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp } // store feasible adducts associated with a cross-link with character nucleotide[0] - vector faa; + vector faa; std::copy(fas.begin(), fas.end(), back_inserter(faa)); ret.feasible_adducts.emplace_back(make_pair(nucleotide, faa)); @@ -3086,7 +3519,7 @@ RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp // Because, e.g., ribose might be a feasible fragment of any nucleotide, we keep only one version // Note: sort by formula and (as tie breaker) the name std::sort(ret.marker_ions.begin(), ret.marker_ions.end(), - [](FragmentAdductDefinition_ const & a, FragmentAdductDefinition_ const & b) + [](RNPxlFragmentAdductDefinition const & a, RNPxlFragmentAdductDefinition const & b) { const String as = a.formula.toString(); const String bs = b.formula.toString(); @@ -3095,7 +3528,7 @@ RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp ); // Note: for uniqueness, we only rely on the formula (in case of tie: keeping the first = shortest name) auto it = std::unique(ret.marker_ions.begin(), ret.marker_ions.end(), - [](FragmentAdductDefinition_ const & a, FragmentAdductDefinition_ const & b) + [](RNPxlFragmentAdductDefinition const & a, RNPxlFragmentAdductDefinition const & b) { return a.formula == b.formula; } @@ -3123,8 +3556,8 @@ RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp return ret; } -void RNPxlSearch::RNPxlFragmentIonGenerator::addMS2MarkerIons( - const vector &marker_ions, +void RNPxlFragmentIonGenerator::addMS2MarkerIons( + const vector &marker_ions, PeakSpectrum &spectrum, PeakSpectrum::IntegerDataArray &spectrum_charge, PeakSpectrum::StringDataArray &spectrum_annotation) @@ -3135,11 +3568,11 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::addMS2MarkerIons( spectrum.emplace_back(mz, 1.0); spectrum_charge.emplace_back(1); - spectrum_annotation.emplace_back(ANNOTATIONS_MARKER_ION_PREFIX + m.name); // add name (e.g., MI:U-H2O) + spectrum_annotation.emplace_back(RNPxlFragmentIonGenerator::ANNOTATIONS_MARKER_ION_PREFIX + m.name); // add name (e.g., MI:U-H2O) } } -void RNPxlSearch::RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( +void RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( const String& unmodified_sequence, PeakSpectrum &spectrum, PeakSpectrum::IntegerDataArray &spectrum_charge, @@ -3169,14 +3602,15 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( } } -void RNPxlSearch::RNPxlFragmentIonGenerator::addShiftedImmoniumIons(const String &unmodified_sequence, + + +void RNPxlFragmentIonGenerator::addShiftedImmoniumIons(const String &unmodified_sequence, const String &fragment_shift_name, const double fragment_shift_mass, PeakSpectrum &partial_loss_spectrum, PeakSpectrum::IntegerDataArray &partial_loss_spectrum_charge, PeakSpectrum::StringDataArray &partial_loss_spectrum_annotation) { - if (unmodified_sequence.hasSubstring("Y")) { const double immonium_ion_mz = EmpiricalFormula("C8H10NO").getMonoWeight() + fragment_shift_mass; @@ -3264,12 +3698,12 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::addShiftedImmoniumIons(const String * and create shifted shifted b,y,a ions + precursors for charge 1..z (adding the unshifted version and performing the shift) * based on the total_loss_spectrum provide to the method */ -void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const String &unmodified_sequence, +void RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const String &unmodified_sequence, const double &fixed_and_variable_modified_peptide_weight, const String &precursor_rna_adduct, const double &precursor_rna_mass, const int &precursor_charge, - const vector &partial_loss_modification, + const vector &partial_loss_modification, const PeakSpectrum& partial_loss_template_z1, const PeakSpectrum& partial_loss_template_z2, const PeakSpectrum& partial_loss_template_z3, @@ -3391,10 +3825,9 @@ void RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const S } partial_loss_spectrum.sortByPosition(); - } -void RNPxlSearch::RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( +void RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( const double fixed_and_variable_modified_peptide_weight, const String &precursor_rna_adduct, const double precursor_rna_mass, @@ -3430,4 +3863,3 @@ int main(int argc, const char** argv) RNPxlSearch tool; return tool.main(argc, argv); } - From 0fe2f67120d2d86c32e9d12e2386b19105f3a636 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 4 Mar 2019 10:26:18 +0100 Subject: [PATCH 020/471] mend --- src/utils/RNPxlSearch.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 5f351845275..3cf1a0da1d0 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -2166,7 +2166,7 @@ static void scoreShiftedFragments_( ExitCodes main_(int, const char**) override { // force initialization of residue db - AASequence::fromString("GPAVLIMCFYWHKRQNEDST"); + static auto s = AASequence::fromString("GPAVLIMCFYWHKRQNEDST"); ProgressLogger progresslogger; progresslogger.setLogType(log_type_); From 3ca454da8e2c76344901711ebaeaff0ceea80e53 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 6 Mar 2019 09:25:22 +0100 Subject: [PATCH 021/471] [FIX] make ResidueDB thread-safe --- .../include/OpenMS/CHEMISTRY/ResidueDB.h | 6 +- src/openms/source/CHEMISTRY/ResidueDB.cpp | 143 +++++++++++------- 2 files changed, 93 insertions(+), 56 deletions(-) diff --git a/src/openms/include/OpenMS/CHEMISTRY/ResidueDB.h b/src/openms/include/OpenMS/CHEMISTRY/ResidueDB.h index 2469d6c342c..8e8ae66ff1f 100644 --- a/src/openms/include/OpenMS/CHEMISTRY/ResidueDB.h +++ b/src/openms/include/OpenMS/CHEMISTRY/ResidueDB.h @@ -71,11 +71,7 @@ namespace OpenMS /// this member function serves as a replacement of the constructor inline static ResidueDB* getInstance() { - static ResidueDB* db_ = nullptr; - if (db_ == nullptr) - { - db_ = new ResidueDB; - } + static ResidueDB* db_ = new ResidueDB; return db_; } diff --git a/src/openms/source/CHEMISTRY/ResidueDB.cpp b/src/openms/source/CHEMISTRY/ResidueDB.cpp index 898c0d9edb9..fe7270227c8 100644 --- a/src/openms/source/CHEMISTRY/ResidueDB.cpp +++ b/src/openms/source/CHEMISTRY/ResidueDB.cpp @@ -64,49 +64,80 @@ namespace OpenMS const Residue* ResidueDB::getResidue(const String& name) const { - if (residue_names_.find(name) != residue_names_.end()) - { - return residue_names_.at(name); - } - return nullptr; + Residue* r(nullptr); + + #pragma omp critical (ResidueDB) + { + auto it = residue_names_.find(name); + if (it != residue_names_.end()) r = it->second; + } + return r; } const Residue* ResidueDB::getResidue(const unsigned char& one_letter_code) const { - return residue_by_one_letter_code_[one_letter_code]; + Residue* r(nullptr); + #pragma omp critical (ResidueDB) + { + r = residue_by_one_letter_code_[one_letter_code]; + } + return r; } Size ResidueDB::getNumberOfResidues() const { - return residues_.size(); + Size s; + #pragma omp critical (ResidueDB) + { + s = residues_.size(); + } + return s; } Size ResidueDB::getNumberOfModifiedResidues() const { - return modified_residues_.size(); + Size s; + #pragma omp critical (ResidueDB) + { + s = modified_residues_.size(); + } + return s; } const set ResidueDB::getResidues(const String& residue_set) const { - if (!residues_by_set_.has(residue_set)) + set s; + #pragma omp critical (ResidueDB) { - throw Exception::ElementNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Residue set cannot be found: '" + residue_set + "'"); - } + // TODO: throwing an exception in parallel loops will lead to problems + // better to just return empty set and handle outside. + if (!residues_by_set_.has(residue_set)) + { + throw Exception::ElementNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Residue set cannot be found: '" + residue_set + "'"); + } + s = residues_by_set_[residue_set]; + } - return residues_by_set_[residue_set]; + return s; } void ResidueDB::setResidues(const String& file_name) { - clearResidues_(); - readResiduesFromFile_(file_name); - buildResidueNames_(); + #pragma omp critical (ResidueDB) + { + clearResidues_(); + readResiduesFromFile_(file_name); + buildResidueNames_(); + } } void ResidueDB::addResidue(const Residue& residue) { - Residue* r = new Residue(residue); - addResidue_(r); + #pragma omp critical (ResidueDB) + { + Residue* r = new Residue(residue); + addResidue_(r); + } } void ResidueDB::addResidue_(Residue* r) @@ -131,7 +162,7 @@ namespace OpenMS for (vector::const_iterator it = names.begin(); it != names.end(); ++it) { residue_names_[*it] = r; - residue_by_one_letter_code_[(unsigned char)(*it)[0]] = r; + residue_by_one_letter_code_[(unsigned char)(r->getOneLetterCode()[0])] = r; } residues_.insert(r); const_residues_.insert(r); @@ -169,21 +200,30 @@ namespace OpenMS bool ResidueDB::hasResidue(const String& res_name) const { - if (residue_names_.find(res_name) != residue_names_.end()) + bool found = false; + #pragma omp critical (ResidueDB) { - return true; - } - return false; + if (residue_names_.find(res_name) != residue_names_.end()) + { + found = true; + } + } + + return found; } bool ResidueDB::hasResidue(const Residue* residue) const { - if (const_residues_.find(residue) != const_residues_.end() || - const_modified_residues_.find(residue) != const_modified_residues_.end()) + bool found = false; + #pragma omp critical (ResidueDB) { - return true; - } - return false; + if (const_residues_.find(residue) != const_residues_.end() || + const_modified_residues_.find(residue) != const_modified_residues_.end()) + { + found = true; + } + } + return found; } void ResidueDB::readResiduesFromFile_(const String& file_name) @@ -408,7 +448,7 @@ namespace OpenMS } const set& ResidueDB::getResidueSets() const - { + { return residue_sets_; } @@ -461,31 +501,32 @@ namespace OpenMS { OPENMS_PRECONDITION(!modification.empty(), "Modification cannot be empty") // search if the mod already exists - String res_name = residue->getName(); - - if (residue_names_.find(res_name) == residue_names_.end()) + const String& res_name = residue->getName(); + Residue* res; + #pragma omp critical (ResidueDB) { - throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, - String("Residue with name " + res_name + " was not registered in residue DB, register first!").c_str()); - } - - // terminal mods. don't apply to residue (side chain), so don't consider them: - const ResidueModification& mod = ModificationsDB::getInstance()->getModification(modification, residue->getOneLetterCode(), ResidueModification::ANYWHERE); - String id = mod.getId(); - if (id.empty()) id = mod.getFullId(); - - if (residue_mod_names_.has(res_name) && residue_mod_names_[res_name].has(id)) - { - return residue_mod_names_[res_name][id]; - } - - Residue* res = new Residue(*residue_names_[res_name]); - res->setModification_(mod); - //res->setLossFormulas(vector()); - //res->setLossNames(vector()); + //TODO: get rid of exception + if (residue_names_.find(res_name) == residue_names_.end()) + { + throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, + String("Residue with name " + res_name + " was not registered in residue DB, register first!").c_str()); + } + // terminal mods. don't apply to residue (side chain), so don't consider them: + const ResidueModification& mod = ModificationsDB::getInstance()->getModification(modification, residue->getOneLetterCode(), ResidueModification::ANYWHERE); + const String& id = mod.getId().empty() ? mod.getFullId() : mod.getId(); - // now register this modified residue - addResidue_(res); + if (residue_mod_names_.has(res_name) && residue_mod_names_[res_name].has(id)) + { + res = residue_mod_names_[res_name][id]; + } + else + { + // create and register this modified residue + res = new Residue(*residue_names_[res_name]); + res->setModification_(mod); + addResidue_(res); + } + } return res; } From dc214dc827363e7ebc25d89f9c304fd805e937b2 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 7 Mar 2019 15:05:34 +0100 Subject: [PATCH 022/471] [FIX] important bugfix - jumbled charge arrays --- src/utils/RNPxlSearch.cpp | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 710dcbf0fa4..2b6a1e7e7d4 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -1286,7 +1286,7 @@ static void scoreShiftedFragments_( // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum // 1. get all possible RNA fragment shifts in the MS2 (based on the precursor RNA/DNA) - LOG_DEBUG << "precursor_rna_adduct: " << precursor_rna_adduct << endl; + LOG_DEBUG << "Precursor NA adduct: " << precursor_rna_adduct << endl; const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; if (feasible_MS2_adducts.empty()) { continue; } // should not be the case - check case of no nucleotide but base fragment ? @@ -1304,6 +1304,11 @@ static void scoreShiftedFragments_( // get marker ions (these are not specific to the cross-linked nucleotide but also depend on the whole oligo bound to the precursor) const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; + LOG_DEBUG << "Marker ions used for this Precursor NA adduct: " << endl; + for (auto & fa : marker_ions) + { + LOG_DEBUG << fa.name << " " << fa.mass << endl; + } // generate total loss spectrum for the fixed and variable modified peptide (without RNA) (using the settings for partial loss generation) // but as we also add the abundant immonium ions for charge 1 and precursor ions for all charges to get a more complete annotation @@ -1551,7 +1556,7 @@ static void scoreShiftedFragments_( fragment_mass_tolerance_unit_ppm, partial_loss_spectrum, exp_spectrum, - total_loss_spectrum.getIntegerDataArrays()[0], + partial_loss_spectrum.getIntegerDataArrays()[0], exp_spectrum.getIntegerDataArrays()[0], ppm_error_array); @@ -1575,10 +1580,16 @@ static void scoreShiftedFragments_( const double & fragment_intensity = fragment.getIntensity(); // in percent (%) const double & fragment_mz = fragment.getMZ(); const int & fragment_charge = exp_spectrum.getIntegerDataArrays().back()[fragment_index]; + #ifdef DEBUG_RNPXLSEARCH + LOG_DEBUG << "fragment_mz:" << fragment_mz << " fragment_charge:" << fragment_charge << endl; + #endif String ion_name = partial_loss_annotations[pair_it->first]; const int charge = partial_loss_charges[pair_it->first]; + #ifdef DEBUG_RNPXLSEARCH + LOG_DEBUG << "theo_name:" << ion_name << " theo_charge:" << charge << endl; + #endif vector f; ion_name.split(' ', f); // e.g. "y3 C3O" or just "y2" @@ -1624,6 +1635,7 @@ static void scoreShiftedFragments_( } else if (ion_name.hasPrefix(RNPxlFragmentIonGenerator::ANNOTATIONS_MARKER_ION_PREFIX)) { + LOG_DEBUG << "Marker ion aligned: " << ion_name << " fragment_mz: " << fragment_mz << " fragment_charge: " << fragment_charge << endl; if (fragment_charge == 1) { PeptideHit::PeakAnnotation fa; From f8acfa424adf4f5a2a5fd06f82244c04d516a68f Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Tue, 19 Mar 2019 13:32:07 +0100 Subject: [PATCH 023/471] :[NOP] add warning if nucleotide modification is repeated --- .../RNPXL/RNPxlModificationsGenerator.cpp | 44 +++++++++++++------ src/utils/RNPxlSearch.cpp | 14 ++++-- 2 files changed, 40 insertions(+), 18 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp index c937106104e..50a206a1ac6 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp @@ -270,7 +270,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse if (sf.second) { // subtractive e = e - mod_ef; - s += "-" + mod; + s += "-" + mod; } else { // additive @@ -278,9 +278,18 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse s += "+" + mod;; } } - actual_combinations.push_back(e); - result.mod_combinations[actual_combinations.back().toString()].insert(s); - LOG_INFO << "\t" << "modifications: " << s << "\t\t" << e.toString() << endl; + + if (find(actual_combinations.begin(), actual_combinations.end(), e) == actual_combinations.end()) + { + actual_combinations.push_back(e); + result.mod_combinations[e.toString()].insert(s); + LOG_INFO << "\t" << "modifications: " << s << "\t\t" << e.toString() << endl; + } + else + { + LOG_WARN << "WARNING:\tNucleotide combination: " << s << "\t\t" << e.toString() + << " occured several times. Did you specify it multiple times in the ini file?. Will consider only once." << endl; + } } } @@ -318,7 +327,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse } } - std::cout << "Filtering on restrictions... " << endl; + LOG_INFO << "Filtering on restrictions... " << endl; // Remove precursor adducts that // 1) do not contain a cross-linkable nucleotide @@ -351,13 +360,20 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse continue; } + // sequence too long + if (nucleotide_style_formula.size() > max_length) + { + violates_restriction.push_back(make_pair(mit->first, s)); + continue; + } + // check if nucleotides from more than one nt_group are present (e.g. from DNA and RNA) Size found_in_n_groups(0); for (const String & n : nt_groups) { if (nucleotide_style_formula.find_first_of(n) != string::npos) { ++found_in_n_groups; } } - // nucleotide stile formula (e.g. AATU matches to more than one group (e.g., RNA and DNA))? + // nucleotide style formula (e.g., AATU matches to more than one group (e.g., RNA and DNA))? if (found_in_n_groups > 1) { violates_restriction.push_back(make_pair(mit->first, s)); @@ -367,7 +383,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse // check if nucleotide is contained in at least one of the target sequences bool containment_violated(false); Size violation_count(0); - for (auto const & current_target_seq : target_sequences) + for (const String & current_target_seq : target_sequences) { if (notInSeq(current_target_seq, nucleotide_style_formula)) { ++violation_count; } } @@ -405,7 +421,6 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse } } - // Optional: add cystein (DTT) adduct if (cysteine_adduct) { @@ -416,19 +431,21 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse // output index -> empirical formula -> (ambiguous) nucleotide formulas // nucleotide formulas which only differ in nucleotide ordering are only printed once // e.g. 5 C19H24N7O12P1 573.122 ( AU-H1O3P1 ) - double pseudo_rt = 1; + double index = 1; for (auto const & m : result.mod_masses) { if (cysteine_adduct && m.first == cysteine_adduct_formula.toString()) { - LOG_INFO << "Precursor adduct " << pseudo_rt++ << "\t:\t" << m.first << " " << m.second << " ( cysteine adduct )" << endl; + LOG_INFO << "Precursor adduct " << index++ << "\t:\t" << m.first << " " << m.second << " ( cysteine adduct )" << endl; continue; } - LOG_INFO << "Precursor adduct " << pseudo_rt++ << "\t:\t" << m.first << " " << m.second << " ( "; + LOG_INFO << "Precursor adduct " << index++ << "\t:\t" << m.first << " " << m.second << " ( "; const set& ambiguities = result.mod_combinations[m.first]; set printed; + + // for all ambiguities (same empirical formula) for (set::const_iterator sit = ambiguities.begin(); sit != ambiguities.end(); ++sit) { String nucleotide_style_formula = *sit; @@ -446,7 +463,6 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse std::sort(nucleotide_style_formula.begin(), nucleotide_style_formula.end()); } - // only print ambiguous sequences once if (printed.find(nucleotide_style_formula) == printed.end()) { @@ -455,10 +471,10 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse } else { - LOG_DEBUG << "ambigious " << nucleotide_style_formula << endl; + LOG_DEBUG << "Same nucleotide composition generated for: " << nucleotide_style_formula + << " will only consider it once to prevent duplicate precursor adducts." << endl; } } - LOG_INFO << ")" << endl; } LOG_INFO << "Finished generation of modification masses." << endl; diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index bb33ea6a9ae..e095ed5f099 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -3279,14 +3279,21 @@ RNPxlParameterParsing::getAllFeasibleFragmentAdducts( const String& ef = pa.first; const set& ambiguities = precursor_adducts.mod_combinations.at(ef); - // for each ambiguous precursor adduct (stored as nucleotide formula e.g.: "AU-H2O") + if (ambiguities.size() >= 2) + { + LOG_DEBUG << "Mods ambiguous on the level of empirical formula: " << endl; + for (auto const & pc_adduct : ambiguities) { LOG_DEBUG << pc_adduct << endl; } + } + + // for each ambiguous (at the level of empirical formula) precursor adduct (stored as nucleotide formula e.g.: "AU-H2O") for (auto const & pc_adduct : ambiguities) { // calculate feasible fragment adducts and store them for lookup - auto feasible_adducts = getFeasibleFragmentAdducts(pc_adduct, ef, nucleotide_to_fragment_adducts, can_xl); + const MS2AdductsOfSinglePrecursorAdduct& feasible_adducts = getFeasibleFragmentAdducts(pc_adduct, ef, nucleotide_to_fragment_adducts, can_xl); // TODO: check if needed anymore - std::sort(feasible_adducts.begin(), feasible_adducts.end()); all_pc_all_feasible_adducts[pc_adduct] = feasible_adducts; - break; // only store one precursor adduct for multiple ambiguities (e.g. AUG, AGU, UAG..) + // only store one precursor adduct for multiple ambiguities (e.g., AUG, AGU, UAG, ...) + break; } } @@ -3614,7 +3621,6 @@ void RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( } - void RNPxlFragmentIonGenerator::addShiftedImmoniumIons(const String &unmodified_sequence, const String &fragment_shift_name, const double fragment_shift_mass, From ae7642e3e5b607e0292add26c15d116ca9a2efdd Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 20 Mar 2019 08:46:54 +0100 Subject: [PATCH 024/471] [FIX] filter ambiguities early --- .../RNPXL/RNPxlModificationsGenerator.cpp | 28 +++++++++++++++++-- src/utils/RNPxlSearch.cpp | 14 +++++++--- 2 files changed, 35 insertions(+), 7 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp index 50a206a1ac6..ffb46eb4c4c 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp @@ -332,6 +332,12 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse // Remove precursor adducts that // 1) do not contain a cross-linkable nucleotide // 2) or contain no cross-linkable nucleotide that is part of the restricted target sequences + // 3) exceed maximum number of nucleotides + + // keep track if a sorted nucleotide composition and modification has already been added + // e.g. we would not add both: UC-H2O-NH3 and CU-NH5O + std::vector > unique_nucleotide_and_mod_composition; + std::vector > violates_restriction; // elemental composition, nucleotide style formula for (Map::ConstIterator mit = result.mod_masses.begin(); mit != result.mod_masses.end(); ++mit) { @@ -349,7 +355,10 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse { nucleotide_style_formula = nucleotide_style_formula.prefix(p); } - + // sort nucleotides so we compare based on nucleotide composition + // e.g.: AC-H2O and CA-H2O are considered the same + std::sort(nucleotide_style_formula.begin(), nucleotide_style_formula.end()); + // check if nucleotide formula contains a cross-linkable amino acid bool has_xl_nt(false); for (auto const & c : nucleotide_style_formula) { if (can_xl.count(c) > 0) { has_xl_nt = true; break;}; } @@ -360,14 +369,14 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse continue; } - // sequence too long + // check if nucleotide sequence too long if (nucleotide_style_formula.size() > max_length) { violates_restriction.push_back(make_pair(mit->first, s)); continue; } - // check if nucleotides from more than one nt_group are present (e.g. from DNA and RNA) + // check if nucleotides from more than one nt_group are present (e.g., from DNA and RNA) Size found_in_n_groups(0); for (const String & n : nt_groups) { @@ -394,6 +403,19 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse { violates_restriction.push_back(make_pair(mit->first, s)); // chemical formula, nucleotide style formula pair violates restrictions } + + // last check: if the sorted nucleotide composition string and mass have already been added + // if so, we don't need to consider that composition again + if ( + find(unique_nucleotide_and_mod_composition.begin(), + unique_nucleotide_and_mod_composition.end(), + make_pair(nucleotide_style_formula, mit->second)) != unique_nucleotide_and_mod_composition.end()) + { + violates_restriction.push_back(make_pair(mit->first, s)); + } + + // record that nucleotide and mod combination has passed all filters and will be considered in further processing + unique_nucleotide_and_mod_composition.push_back({nucleotide_style_formula, mit->second}); } } diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index e095ed5f099..6077337fb4a 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -2258,7 +2258,7 @@ static void scoreShiftedFragments_( bool cysteine_adduct = getFlag_("RNPxl:CysteineAdduct"); - // generate all precursor adducts + // generate mapping from empirical formula to mass and empirical formula to (one or more) precursor adducts RNPxlModificationMassesResult mm; if (max_nucleotide_length != 0) { @@ -3273,15 +3273,16 @@ RNPxlParameterParsing::getAllFeasibleFragmentAdducts( { PrecursorsToMS2Adducts all_pc_all_feasible_adducts; - // for all possible precursor adducts + // for all distinct precursor adduct formulas/masses for (auto const & pa : precursor_adducts.mod_masses) { + // get all precursor nucleotide formulas matching current empirical formula/mass const String& ef = pa.first; const set& ambiguities = precursor_adducts.mod_combinations.at(ef); if (ambiguities.size() >= 2) { - LOG_DEBUG << "Mods ambiguous on the level of empirical formula: " << endl; + LOG_DEBUG << ambiguities.size() << " nucleotide formulas are ambiguous on the level of empirical formula: " << endl; for (auto const & pc_adduct : ambiguities) { LOG_DEBUG << pc_adduct << endl; } } @@ -3293,7 +3294,12 @@ RNPxlParameterParsing::getAllFeasibleFragmentAdducts( // TODO: check if needed anymore - std::sort(feasible_adducts.begin(), feasible_adducts.end()); all_pc_all_feasible_adducts[pc_adduct] = feasible_adducts; // only store one precursor adduct for multiple ambiguities (e.g., AUG, AGU, UAG, ...) - break; + break; + // + // TODO!!!!!!!!! get rid of break (properly) + // 1. make sure that nucleotide permutations are discarded + // 2. but keep different nucleotide combinations resulting in same empirical formula + // } } From f0d4d57418512ec42e7406aa9b07a99a3165e25a Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 20 Mar 2019 08:55:45 +0100 Subject: [PATCH 025/471] :[FIX] generale all precursor adducts even if they have same mass and potentially same fragment adducts (are kind of indistinguishable) --- src/utils/RNPxlSearch.cpp | 66 +++++++++++++++++++++++++++++---------- 1 file changed, 49 insertions(+), 17 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 6077337fb4a..da19e0abc0a 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -100,7 +100,7 @@ using namespace OpenMS; using namespace OpenMS::Internal; using namespace std; - // stores which residues (known to give rise to immonium ions) are in the sequence +// stores which residues (known to give rise to immonium ions) are in the sequence struct ImmoniumIonsInPeptide { ImmoniumIonsInPeptide(const String& s) @@ -3236,9 +3236,8 @@ static void scoreShiftedFragments_( } }; - - -vector RNPxlParameterParsing::getModifications(StringList modNames) { +vector RNPxlParameterParsing::getModifications(StringList modNames) +{ vector modifications; // iterate over modification names and add to vector @@ -3267,17 +3266,25 @@ vector RNPxlParameterParsing::getModifications(StringList m RNPxlParameterParsing::PrecursorsToMS2Adducts RNPxlParameterParsing::getAllFeasibleFragmentAdducts( - const RNPxlModificationMassesResult &precursor_adducts, - const RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, - const set &can_xl) + const RNPxlModificationMassesResult & precursor_adducts, + const RNPxlParameterParsing::NucleotideToFragmentAdductMap & nucleotide_to_fragment_adducts, + const set & can_xl) { PrecursorsToMS2Adducts all_pc_all_feasible_adducts; + map pc2mass; + map pc2ef; + + using PrecursorAdductMassAndMS2Fragments = pair>; + using PrecursorAdductAndXLNucleotide = pair; + map> mass_frags2pc_xlnuc; + // for all distinct precursor adduct formulas/masses for (auto const & pa : precursor_adducts.mod_masses) { // get all precursor nucleotide formulas matching current empirical formula/mass const String& ef = pa.first; + const double pc_mass = pa.second; const set& ambiguities = precursor_adducts.mod_combinations.at(ef); if (ambiguities.size() >= 2) @@ -3287,30 +3294,38 @@ RNPxlParameterParsing::getAllFeasibleFragmentAdducts( } // for each ambiguous (at the level of empirical formula) precursor adduct (stored as nucleotide formula e.g.: "AU-H2O") - for (auto const & pc_adduct : ambiguities) + for (const String & pc_adduct : ambiguities) { // calculate feasible fragment adducts and store them for lookup const MS2AdductsOfSinglePrecursorAdduct& feasible_adducts = getFeasibleFragmentAdducts(pc_adduct, ef, nucleotide_to_fragment_adducts, can_xl); // TODO: check if needed anymore - std::sort(feasible_adducts.begin(), feasible_adducts.end()); - all_pc_all_feasible_adducts[pc_adduct] = feasible_adducts; - // only store one precursor adduct for multiple ambiguities (e.g., AUG, AGU, UAG, ...) - break; - // - // TODO!!!!!!!!! get rid of break (properly) - // 1. make sure that nucleotide permutations are discarded - // 2. but keep different nucleotide combinations resulting in same empirical formula - // + all_pc_all_feasible_adducts[pc_adduct] = feasible_adducts; + pc2mass[pc_adduct] = pc_mass; + pc2ef[pc_adduct] = ef; } } // print feasible fragment adducts and marker ions for (auto const & fa : all_pc_all_feasible_adducts) { - LOG_DEBUG << "Precursor adduct: " << fa.first << "\n"; + const String & pc = fa.first; + LOG_DEBUG << "Precursor adduct: " << pc << "\t" << pc2ef[pc] << "\t" << pc2mass[pc] << "\n"; + + // collect set of masses to detect ambiguities + set mi_fragments; + for (auto const & mis : fa.second.marker_ions) { mi_fragments.insert(mis.mass); } for (auto const & ffa : fa.second.feasible_adducts) { const char & nucleotide = ffa.first; + set fragments; + for (auto const & f : mi_fragments) { fragments.insert(f); } // copy over common marker ion masses + for (auto const & f : ffa.second) { fragments.insert(f.mass); } // copy over xl-ed nucleotide associated fragment masses + // we want to track if a certain MS1 mass and set of MS2 ions allow to distinguish + // (at least in theory) precursor adduct and cross-linked nucleotide + // to do so, we map mass and set of fragment ions to precursor adduct and cross-linked nucleotide + mass_frags2pc_xlnuc[{pc2mass[pc], fragments}].push_back({pc, nucleotide}); + LOG_DEBUG << " Cross-linkable nucleotide '" << nucleotide << "' and feasible fragment adducts:" << endl; for (auto const & a : ffa.second) { @@ -3326,6 +3341,23 @@ RNPxlParameterParsing::getAllFeasibleFragmentAdducts( } LOG_DEBUG << endl; + // report precursor adducts/cross-linked nucleotide combinations with same mass that produce the exact same MS2 ions as indistinguishable + for (auto const & f : mass_frags2pc_xlnuc) + { + if (f.second.size() > 1) + { + LOG_INFO << "Theoretical indistinguishable cross-links detected: " << endl; + for (auto const & m : f.second) + { + LOG_INFO << "Precursor: " << m.first << "\t and cross-linked nucleotide: " << m.second << endl; + for (auto const & fragment_mass : f.first.second) + { + LOG_INFO << "Fragment mass: " << fragment_mass << endl; + } + } + } + } + return all_pc_all_feasible_adducts; } From a83d3458ead14b2f800d6e5683e988a325388984 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 20 Mar 2019 14:04:48 +0100 Subject: [PATCH 026/471] [REFACTOR] move some code into extra files --- .../RNPXL/RNPxlFragmentAdductDefinition.h | 78 ++ .../RNPXL/RNPxlFragmentAnnotationHelper.h | 3 - .../RNPXL/RNPxlFragmentIonGenerator.h | 101 +++ .../ANALYSIS/RNPXL/RNPxlParameterParsing.h | 100 ++ .../OpenMS/ANALYSIS/RNPXL/sources.cmake | 3 + .../RNPXL/RNPxlFragmentAdductDefinition.cpp | 44 + .../RNPXL/RNPxlFragmentAnnotationHelper.cpp | 1 - .../RNPXL/RNPxlFragmentIonGenerator.cpp | 349 +++++++ .../ANALYSIS/RNPXL/RNPxlParameterParsing.cpp | 427 +++++++++ .../source/ANALYSIS/RNPXL/sources.cmake | 3 + src/utils/RNPxlSearch.cpp | 853 +----------------- 11 files changed, 1133 insertions(+), 829 deletions(-) create mode 100644 src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAdductDefinition.h create mode 100644 src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentIonGenerator.h create mode 100644 src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlParameterParsing.h create mode 100644 src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAdductDefinition.cpp create mode 100644 src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentIonGenerator.cpp create mode 100644 src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAdductDefinition.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAdductDefinition.h new file mode 100644 index 00000000000..22537620744 --- /dev/null +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAdductDefinition.h @@ -0,0 +1,78 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2018. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace OpenMS +{ +struct OPENMS_DLLAPI RNPxlFragmentAdductDefinition +{ + EmpiricalFormula formula; // formula + String name; // name used in annotation + double mass = 0; + + RNPxlFragmentAdductDefinition() = default; + + RNPxlFragmentAdductDefinition(const RNPxlFragmentAdductDefinition&) = default; + + RNPxlFragmentAdductDefinition(RNPxlFragmentAdductDefinition&&) = default; + + RNPxlFragmentAdductDefinition& operator=(const RNPxlFragmentAdductDefinition&) = default; + + RNPxlFragmentAdductDefinition& operator=(RNPxlFragmentAdductDefinition&&) = default; + + bool operator<(const RNPxlFragmentAdductDefinition& other) const + { + String fa = formula.toString(); + String fb = other.formula.toString(); + return std::tie(mass, fa, name) < std::tie(other.mass, fb, other.name); + } + + bool operator==(const RNPxlFragmentAdductDefinition& other) const + { + return std::tie(formula, name) == std::tie(other.formula, other.name); + } +}; + +} + diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h index 17a2720babd..512f8dca2d6 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h @@ -46,8 +46,6 @@ namespace OpenMS { -namespace Internal -{ /* @brief Convenience functions to construct appealing fragment annotation strings * and store them as PeptideHit::PeakAnnotation @@ -107,7 +105,6 @@ class OPENMS_DLLAPI RNPxlFragmentAnnotationHelper const std::vector& annotated_precursor_ions, std::vector& fas); }; -} // namespace Internal } // namespace OpenMS diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentIonGenerator.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentIonGenerator.h new file mode 100644 index 00000000000..402a8f8679a --- /dev/null +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentIonGenerator.h @@ -0,0 +1,101 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2018. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace OpenMS +{ + +// helper class that adds special ions not covered by TheoreticalSpectrumGenerator +class OPENMS_DLLAPI RNPxlFragmentIonGenerator +{ + public: + // prefix used to denote marker ions in fragment annotations + static constexpr const char* ANNOTATIONS_MARKER_ION_PREFIX = "MI:"; + + // add RNA-marker ions of charge 1 + // this includes the protonated nitrogenous base and all shifts (e.g., U-H2O, U'-H20, ...) + static void addMS2MarkerIons( + const std::vector& marker_ions, + PeakSpectrum& spectrum, + PeakSpectrum::IntegerDataArray& spectrum_charge, + PeakSpectrum::StringDataArray& spectrum_annotation); + + static void addShiftedImmoniumIons( + const String & unmodified_sequence, + const String & fragment_shift_name, + const double fragment_shift_mass, + PeakSpectrum & partial_loss_spectrum, + PeakSpectrum::IntegerDataArray& partial_loss_spectrum_charge, + PeakSpectrum::StringDataArray& partial_loss_spectrum_annotation); + + static void generatePartialLossSpectrum(const String& unmodified_sequence, + const double& fixed_and_variable_modified_peptide_weight, + const String& precursor_rna_adduct, + const double& precursor_rna_mass, + const int& precursor_charge, + const std::vector& partial_loss_modification, + const PeakSpectrum& patial_loss_template_z1, + const PeakSpectrum& patial_loss_template_z2, + const PeakSpectrum& patial_loss_template_z3, + PeakSpectrum& partial_loss_spectrum); + static void addPrecursorWithCompleteRNA_(const double fixed_and_variable_modified_peptide_weight, + const String & precursor_rna_adduct, + const double precursor_rna_mass, + const int charge, + PeakSpectrum & partial_loss_spectrum, + MSSpectrum::IntegerDataArray & partial_loss_spectrum_charge, + MSSpectrum::StringDataArray & partial_loss_spectrum_annotation); + + static void addSpecialLysImmonumIons(const String& unmodified_sequence, + PeakSpectrum &spectrum, + PeakSpectrum::IntegerDataArray &spectrum_charge, + PeakSpectrum::StringDataArray &spectrum_annotation); +}; + + +} + diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlParameterParsing.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlParameterParsing.h new file mode 100644 index 00000000000..fbfa9166bd8 --- /dev/null +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlParameterParsing.h @@ -0,0 +1,100 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2018. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace OpenMS +{ + +// fast (flat) data structure to store feasible x-,y-,a-ion fragment adducts and observable marker ions +using NucleotideToFeasibleFragmentAdducts = std::pair >; + +// stores the fragment adducts and marker ions for a given precursor adduct +struct OPENMS_DLLAPI MS2AdductsOfSinglePrecursorAdduct +{ + std::vector feasible_adducts; + std::vector marker_ions; +}; + +// helper struct to facilitate parsing of parameters (modifications, nucleotide adducts, ...) +struct OPENMS_DLLAPI RNPxlParameterParsing +{ + /// Query ResidueModifications (given as strings) from ModificationsDB + static std::vector getModifications(StringList modNames); + + // Map a nucleotide (e.g. U to all possible fragment adducts) + using NucleotideToFragmentAdductMap = std::map >; + // @brief Parse tool parameter to create map from target nucleotide to all its fragment adducts + // It maps a single letter nucleotide (e.g., 'T', 'C', ...) + // to the maximum set of fragment adducts that may arise if the nucleotide is cross-linked. + // Losses, that might reduce this set, are not considered in this data structure and handled later + // when specific precursor adducts are considered. + static NucleotideToFragmentAdductMap getTargetNucleotideToFragmentAdducts(StringList fragment_adducts); + + // @brief Determines the fragment adducts and marker ions for a given precursor. + // The precursor adduct (the oligo including losses, e.g.: "TC-H3PO4") is mapped to all contained nucleotides + // and their marker ions. In addition, each cross-linkable nucleotide is mapped to its chemically feasible fragment adducts. + // Chemical feasible means in this context, that the fragment or marker ion adduct is a subformula of the precursor adduct. + static MS2AdductsOfSinglePrecursorAdduct getFeasibleFragmentAdducts( + const String& exp_pc_adduct, + const String& exp_pc_formula, + const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, + const std::set& can_xl + ); + + // Maps a precursor adduct (e.g.: "UU-H2O") to all chemically feasible fragment adducts. + using PrecursorsToMS2Adducts = std::map; + + // @brief Calculate all chemically feasible fragment adducts for all possible precursor adducts + // Same as getFeasibleFragmentAdducts but calculated from all precursor adducts + static PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts( + const RNPxlModificationMassesResult& precursor_adducts, + const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, + const std::set& can_xl); +}; + +} + diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake b/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake index 52bbb7b7a0e..b42debfbb9e 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake @@ -7,9 +7,12 @@ HyperScore.h ModifiedPeptideGenerator.h MorpheusScore.h PScore.h +RNPxlFragmentAdductDefinition.h RNPxlFragmentAnnotationHelper.h +RNPxlFragmentIonGenerator.h RNPxlMarkerIonExtractor.h RNPxlModificationsGenerator.h +RNPxlParameterParsing.h RNPxlReport.h ) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAdductDefinition.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAdductDefinition.cpp new file mode 100644 index 00000000000..85624b39067 --- /dev/null +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAdductDefinition.cpp @@ -0,0 +1,44 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2018. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#include + +using namespace std; + +namespace OpenMS +{ + + +} + diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.cpp index 3c4e062361b..86122b4a3c8 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.cpp @@ -43,7 +43,6 @@ #include using namespace OpenMS; -using namespace OpenMS::Internal; namespace OpenMS diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentIonGenerator.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentIonGenerator.cpp new file mode 100644 index 00000000000..f21c0fc201c --- /dev/null +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlFragmentIonGenerator.cpp @@ -0,0 +1,349 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2018. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#include +#include +#include +#include +#include +#include +#include + +using namespace std; + +namespace OpenMS +{ +void RNPxlFragmentIonGenerator::addMS2MarkerIons( + const std::vector &marker_ions, + PeakSpectrum &spectrum, + PeakSpectrum::IntegerDataArray &spectrum_charge, + PeakSpectrum::StringDataArray &spectrum_annotation) +{ + for (auto const & m : marker_ions) + { + const double mz = m.mass + Constants::PROTON_MASS_U; + + spectrum.emplace_back(mz, 1.0); + spectrum_charge.emplace_back(1); + spectrum_annotation.emplace_back(RNPxlFragmentIonGenerator::ANNOTATIONS_MARKER_ION_PREFIX + m.name); // add name (e.g., MI:U-H2O) + } +} + +void RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( + const String& unmodified_sequence, + PeakSpectrum &spectrum, + PeakSpectrum::IntegerDataArray &spectrum_charge, + PeakSpectrum::StringDataArray &spectrum_annotation) +{ + if (unmodified_sequence.has('K')) + { + const double immonium_ion2_mz = EmpiricalFormula("C5H10N1").getMonoWeight(); + // only add special ios if there is not already a peak + if (spectrum.findNearest(immonium_ion2_mz, 1e-4) == -1) + { + spectrum.emplace_back(immonium_ion2_mz, 1.0); + spectrum_charge.emplace_back(1); + spectrum_annotation.emplace_back(String("iK(C5H10N1)")); + } + + // usually only observed without shift (A. Stuetzer) + const double immonium_ion3_mz = EmpiricalFormula("C6H13N2O").getMonoWeight(); + // only add special ios if there is not already a peak + if (spectrum.findNearest(immonium_ion3_mz, 1e-4) == -1) + { + spectrum.emplace_back(immonium_ion3_mz, 1.0); + spectrum_charge.emplace_back(1); + spectrum_annotation.emplace_back(String("iK(C6H13N2O)")); + } + + } +} + + +void RNPxlFragmentIonGenerator::addShiftedImmoniumIons(const String &unmodified_sequence, + const String &fragment_shift_name, + const double fragment_shift_mass, + PeakSpectrum &partial_loss_spectrum, + PeakSpectrum::IntegerDataArray &partial_loss_spectrum_charge, + PeakSpectrum::StringDataArray &partial_loss_spectrum_annotation) +{ + if (unmodified_sequence.hasSubstring("Y")) + { + const double immonium_ion_mz = EmpiricalFormula("C8H10NO").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('Y', fragment_shift_name)); + } + else if (unmodified_sequence.hasSubstring("W")) + { + const double immonium_ion_mz = EmpiricalFormula("C10H11N2").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('W', fragment_shift_name)); + } + else if (unmodified_sequence.hasSubstring("F")) + { + const double immonium_ion_mz = EmpiricalFormula("C8H10N").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('F', fragment_shift_name)); + } + else if (unmodified_sequence.hasSubstring("H")) + { + const double immonium_ion_mz = EmpiricalFormula("C5H8N3").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('H', fragment_shift_name)); + } + else if (unmodified_sequence.hasSubstring("C")) + { + const double immonium_ion_mz = EmpiricalFormula("C2H6NS").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('C', fragment_shift_name)); + } + else if (unmodified_sequence.hasSubstring("P")) + { + const double immonium_ion_mz = EmpiricalFormula("C4H8N").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('P', fragment_shift_name)); + } + else if (unmodified_sequence.hasSubstring("L") || unmodified_sequence.hasSubstring("I")) + { + const double immonium_ion_mz = EmpiricalFormula("C5H12N").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('L', fragment_shift_name)); + } + else if (unmodified_sequence.hasSubstring("K")) + { + // classical immonium ion + const double immonium_ion_mz = EmpiricalFormula("C5H13N2").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('K', fragment_shift_name)); + + // TODO: check if only DNA specific and if also other shifts are observed + // according to A. Stuetzer mainly observed with C‘-NH3 (94.0167 Da) + const double immonium_ion2_mz = EmpiricalFormula("C5H10N1").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion2_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(String("iK(C5H10N1)" + fragment_shift_name)); + + // usually only observed without shift (A. Stuetzer) + const double immonium_ion3_mz = EmpiricalFormula("C6H13N2O").getMonoWeight() + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion3_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(String("iK(C6H13N2O)" + fragment_shift_name)); + } + else if (unmodified_sequence.hasSubstring("M")) + { + const double immonium_ion_mz = 104.05285 + fragment_shift_mass; + partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); + partial_loss_spectrum_charge.emplace_back(1); + partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('M', fragment_shift_name)); + } +} + + /* + * Add peaks with shifts induced by the RNA/DNA: + * - Precursor with complete NA-oligo for charge 1..z + * - Partial shifts (without complete precursor adduct) + * - Add shifted immonium ions for charge 1 only + * and create shifted shifted b,y,a ions + precursors for charge 1..z (adding the unshifted version and performing the shift) + * based on the total_loss_spectrum provide to the method + */ +void RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const String &unmodified_sequence, + const double &fixed_and_variable_modified_peptide_weight, + const String &precursor_rna_adduct, + const double &precursor_rna_mass, + const int &precursor_charge, + const std::vector &partial_loss_modification, + const PeakSpectrum& partial_loss_template_z1, + const PeakSpectrum& partial_loss_template_z2, + const PeakSpectrum& partial_loss_template_z3, + PeakSpectrum &partial_loss_spectrum) +{ + partial_loss_spectrum.getIntegerDataArrays().resize(1); + PeakSpectrum::IntegerDataArray& partial_loss_spectrum_charge = partial_loss_spectrum.getIntegerDataArrays()[0]; + + partial_loss_spectrum.getStringDataArrays().resize(1); // annotation + PeakSpectrum::StringDataArray& partial_loss_spectrum_annotation = partial_loss_spectrum.getStringDataArrays()[0]; + + // for all observable MS2 adducts ... + for (Size i = 0; i != partial_loss_modification.size(); ++i) + { + // get name and mass of fragment adduct + const String& fragment_shift_name = partial_loss_modification[i].name; // e.g. U-H2O + const double fragment_shift_mass = partial_loss_modification[i].mass; + + // ADD: shifted immonium ion peaks of charge 1 (if the amino acid is present in the sequence) + RNPxlFragmentIonGenerator::addShiftedImmoniumIons( + unmodified_sequence, + fragment_shift_name, + fragment_shift_mass, + partial_loss_spectrum, + partial_loss_spectrum_charge, + partial_loss_spectrum_annotation); + + // annotate generated a-,b-,y-ions with fragment shift name + PeakSpectrum shifted_series_peaks; + shifted_series_peaks.getStringDataArrays().resize(1); // annotation + shifted_series_peaks.getIntegerDataArrays().resize(1); // charge + + PeakSpectrum::StringDataArray& shifted_series_annotations = shifted_series_peaks.getStringDataArrays()[0]; + PeakSpectrum::IntegerDataArray& shifted_series_charges = shifted_series_peaks.getIntegerDataArrays()[0]; + + // For every charge state + for (int z = 1; z <= precursor_charge; ++z) + { + // 1. add shifted peaks + if (z == 1) + { + for (Size i = 0; i != partial_loss_template_z1.size(); ++i) + { + Peak1D p = partial_loss_template_z1[i]; + p.setMZ(p.getMZ() + fragment_shift_mass); + shifted_series_peaks.push_back(p); + shifted_series_annotations.push_back(partial_loss_template_z1.getStringDataArrays()[0][i]); + shifted_series_charges.push_back(1); + } + } + else if (z == 2) + { + for (Size i = 0; i != partial_loss_template_z2.size(); ++i) + { + // currently, also contains z=1 precursor peaks which we aleardy added before + if (partial_loss_template_z2.getIntegerDataArrays()[0][i] == 2) + { + Peak1D p = partial_loss_template_z2[i]; + p.setMZ(p.getMZ() + fragment_shift_mass / 2.0); + shifted_series_peaks.push_back(p); + shifted_series_annotations.push_back(partial_loss_template_z2.getStringDataArrays()[0][i]); + shifted_series_charges.push_back(2); + } + } + } + else if (z == 3) + { + for (Size i = 0; i != partial_loss_template_z3.size(); ++i) + { + // currently, also contains z=1 and 2 precursor peaks which we aleardy added before + if (partial_loss_template_z3.getIntegerDataArrays()[0][i] == 3) + { + Peak1D p = partial_loss_template_z3[i]; + p.setMZ(p.getMZ() + fragment_shift_mass / 3.0); + shifted_series_peaks.push_back(p); + shifted_series_annotations.push_back(partial_loss_template_z3.getStringDataArrays()[0][i]); + shifted_series_charges.push_back(3); + } + } + } + else // don't consider fragment ions with charge >= 4 + { + break; + } + } + + // 2. add fragment shift name to annotation of shifted peaks + for (Size j = 0; j != shifted_series_annotations.size(); ++j) + { + shifted_series_annotations[j] += " " + fragment_shift_name; + } + + // append shifted and annotated ion series to partial loss spectrum + partial_loss_spectrum.insert(partial_loss_spectrum.end(), + shifted_series_peaks.begin(), shifted_series_peaks.end()); + // std::move strings during insert + partial_loss_spectrum_annotation.insert( + partial_loss_spectrum_annotation.end(), + make_move_iterator(shifted_series_annotations.begin()), + make_move_iterator(shifted_series_annotations.end()) + ); + partial_loss_spectrum.getIntegerDataArrays()[0].insert( + partial_loss_spectrum_charge.end(), + shifted_series_charges.begin(), + shifted_series_charges.end() + ); + } + + // ADD: (mainly for ETD) MS2 precursor peaks of the MS1 adduct (total RNA) carrying peptide for all z <= precursor charge + for (int charge = 1; charge <= static_cast(precursor_charge); ++charge) + { + addPrecursorWithCompleteRNA_(fixed_and_variable_modified_peptide_weight, + precursor_rna_adduct, + precursor_rna_mass, + charge, + partial_loss_spectrum, + partial_loss_spectrum_charge, + partial_loss_spectrum_annotation); + } + + partial_loss_spectrum.sortByPosition(); +} + +void RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( + const double fixed_and_variable_modified_peptide_weight, + const String &precursor_rna_adduct, + const double precursor_rna_mass, + const int charge, + PeakSpectrum &partial_loss_spectrum, + MSSpectrum::IntegerDataArray &partial_loss_spectrum_charge, + MSSpectrum::StringDataArray &partial_loss_spectrum_annotation) +{ + const double xl_mz = (fixed_and_variable_modified_peptide_weight + precursor_rna_mass + + static_cast(charge) * Constants::PROTON_MASS_U) + / static_cast(charge); + + // only add special ions if there is not already a peak + if (partial_loss_spectrum.findNearest(xl_mz, 1e-4) == -1) + { + partial_loss_spectrum.push_back(Peak1D(xl_mz, 1.0)); + partial_loss_spectrum_charge.push_back(charge); + if (charge > 1) + { + partial_loss_spectrum_annotation.push_back(String("[M+") + + String(charge) + "H+" + precursor_rna_adduct + "]"); + } + else + { + partial_loss_spectrum_annotation.push_back(String("[M+H+") + + precursor_rna_adduct + "]"); + } + } +} + +} + diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp new file mode 100644 index 00000000000..482fe40350c --- /dev/null +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp @@ -0,0 +1,427 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2018. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#include +#include +#include +#include +#include +#include + +using namespace std; + +namespace OpenMS +{ + +RNPxlParameterParsing::PrecursorsToMS2Adducts +RNPxlParameterParsing::getAllFeasibleFragmentAdducts( + const RNPxlModificationMassesResult & precursor_adducts, + const RNPxlParameterParsing::NucleotideToFragmentAdductMap & nucleotide_to_fragment_adducts, + const set & can_xl) +{ + PrecursorsToMS2Adducts all_pc_all_feasible_adducts; + + map pc2mass; + map pc2ef; + + using PrecursorAdductMassAndMS2Fragments = pair>; + using PrecursorAdductAndXLNucleotide = pair; + map> mass_frags2pc_xlnuc; + + // for all distinct precursor adduct formulas/masses + for (auto const & pa : precursor_adducts.mod_masses) + { + // get all precursor nucleotide formulas matching current empirical formula/mass + const String& ef = pa.first; + const double pc_mass = pa.second; + const set& ambiguities = precursor_adducts.mod_combinations.at(ef); + + if (ambiguities.size() >= 2) + { + LOG_DEBUG << ambiguities.size() << " nucleotide formulas are ambiguous on the level of empirical formula: " << endl; + for (auto const & pc_adduct : ambiguities) { LOG_DEBUG << pc_adduct << endl; } + } + + // for each ambiguous (at the level of empirical formula) precursor adduct (stored as nucleotide formula e.g.: "AU-H2O") + for (const String & pc_adduct : ambiguities) + { + // calculate feasible fragment adducts and store them for lookup + const MS2AdductsOfSinglePrecursorAdduct& feasible_adducts = getFeasibleFragmentAdducts(pc_adduct, ef, nucleotide_to_fragment_adducts, can_xl); + // TODO: check if needed anymore - std::sort(feasible_adducts.begin(), feasible_adducts.end()); + all_pc_all_feasible_adducts[pc_adduct] = feasible_adducts; + pc2mass[pc_adduct] = pc_mass; + pc2ef[pc_adduct] = ef; + } + } + + // print feasible fragment adducts and marker ions + for (auto const & fa : all_pc_all_feasible_adducts) + { + const String & pc = fa.first; + LOG_DEBUG << "Precursor adduct: " << pc << "\t" << pc2ef[pc] << "\t" << pc2mass[pc] << "\n"; + + // collect set of masses to detect ambiguities + set mi_fragments; + for (auto const & mis : fa.second.marker_ions) { mi_fragments.insert(mis.mass); } + + for (auto const & ffa : fa.second.feasible_adducts) + { + const char & nucleotide = ffa.first; + set fragments; + for (auto const & f : mi_fragments) { fragments.insert(f); } // copy over common marker ion masses + for (auto const & f : ffa.second) { fragments.insert(f.mass); } // copy over xl-ed nucleotide associated fragment masses + // we want to track if a certain MS1 mass and set of MS2 ions allow to distinguish + // (at least in theory) precursor adduct and cross-linked nucleotide + // to do so, we map mass and set of fragment ions to precursor adduct and cross-linked nucleotide + mass_frags2pc_xlnuc[{pc2mass[pc], fragments}].push_back({pc, nucleotide}); + + LOG_DEBUG << " Cross-linkable nucleotide '" << nucleotide << "' and feasible fragment adducts:" << endl; + for (auto const & a : ffa.second) + { + LOG_DEBUG << " " << a.name << "\t" << a.formula.toString() << "\t" << a.mass << "\n"; + } + } + + LOG_DEBUG << " Marker ions." << endl; + for (auto const & ffa : fa.second.marker_ions) + { + LOG_DEBUG << " " << ffa.name << "\t" << ffa.formula.toString() << "\t" << ffa.mass << "\n"; + } + } + LOG_DEBUG << endl; + + // report precursor adducts/cross-linked nucleotide combinations with same mass that produce the exact same MS2 ions as indistinguishable + // e.g., for nucleotides that only produce ribose fragments there might be a lot of overlap + for (auto const & f : mass_frags2pc_xlnuc) + { + if (f.second.size() > 1) + { + LOG_INFO << "Theoretical indistinguishable cross-link adducts detected: " << endl; + for (auto const & m : f.second) + { + LOG_INFO << "\tPrecursor: " << m.first << "\t and cross-linked nucleotide: " << m.second << endl; + for (auto const & fragment_mass : f.first.second) + { + LOG_INFO << "\tFragment mass: " << fragment_mass << endl; + } + } + } + } + + return all_pc_all_feasible_adducts; +} + +RNPxlParameterParsing::NucleotideToFragmentAdductMap +RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringList fragment_adducts) +{ + NucleotideToFragmentAdductMap nucleotide_to_fragment_adducts; + for (String t : fragment_adducts) + { + t.removeWhitespaces(); + + EmpiricalFormula formula; + String name; + + // format is: target_nucletide:formula;name + char target_nucleotide = t[0]; + if (t[1] != ':') + { + LOG_WARN << "Missing ':'. Wrong format of fragment_adduct string: " << t << endl; + return NucleotideToFragmentAdductMap(); + } + + // remove target nucleotide and : character from t + t = t.substr(2); + + // split into formula and name + vector fs; + t.split(";", fs); + if (fs.size() == 1) // no name provided so we just take the formula as name + { + formula = EmpiricalFormula(fs[0]); + name = formula.toString(); + } + else if (fs.size() == 2) + { + formula = EmpiricalFormula(fs[0]); + name = fs[1]; + } + else + { + LOG_WARN << "Wrong format of fragment_adduct string: " << t << endl; + return NucleotideToFragmentAdductMap(); + } + + RNPxlFragmentAdductDefinition fad; + fad.name = name; + fad.formula = formula; + fad.mass = formula.getMonoWeight(); + + nucleotide_to_fragment_adducts[target_nucleotide].insert(fad); + + // register all fragment adducts as N- and C-terminal modification (if not already registered) + if (!ModificationsDB::getInstance()->has(name)) + { + ResidueModification * c_term = new ResidueModification(); + c_term->setId(name); + c_term->setName(name); + c_term->setFullId(name + " (C-term)"); + c_term->setTermSpecificity(ResidueModification::C_TERM); + c_term->setDiffMonoMass(fad.mass); + ModificationsDB::getInstance()->addModification(c_term); + + ResidueModification * n_term = new ResidueModification(); + n_term->setId(name); + n_term->setName(name); + n_term->setFullId(name + " (N-term)"); + n_term->setTermSpecificity(ResidueModification::N_TERM); + n_term->setDiffMonoMass(fad.mass); + ModificationsDB::getInstance()->addModification(n_term); + } + } + +#ifdef DEBUG_RNPXLSEARCH + for (auto const & p2fas : precursor_to_fragment_adducts) + { + for (auto const & p2fa : p2fas.second) + { + cout << "nucleotide:" << p2fas.first + << " fragment adduct:" << p2fa.formula.toString() + << " fragment adduct mass:" << p2fa.mass + << " name:" << p2fa.name << endl; + } + } +#endif + + return nucleotide_to_fragment_adducts; +} + +MS2AdductsOfSinglePrecursorAdduct +RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, + const String &exp_pc_formula, + const RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, + const set &can_xl) +{ + LOG_DEBUG << "Generating fragment adducts for precursor adduct: '" << exp_pc_adduct << "'" << endl; + + MS2AdductsOfSinglePrecursorAdduct ret; + + // no precursor adduct? + if (exp_pc_formula.empty()) { return ret; } // no fragment adducts or marker ions are expected! + + // count nucleotides in precursor adduct (e.g.: "TCA-H2O" yields map: T->1, C->1, A->1) + // and determine the set of cross-linkable nucleotides in the precursor adduct + size_t nt_count(0); + map exp_pc_nucleotide_count; + set exp_pc_xl_nts; + String::const_iterator exp_pc_it = exp_pc_adduct.begin(); + for (; exp_pc_it != exp_pc_adduct.end(); ++exp_pc_it, ++nt_count) + { + // we are finished with nucleotides in string if first loss/gain is encountered + if (*exp_pc_it == '+' || *exp_pc_it == '-') break; + + // count occurence of nucleotide + if (exp_pc_nucleotide_count.count(*exp_pc_it) == 0) + { + exp_pc_nucleotide_count[*exp_pc_it] = 1; + if (can_xl.count(*exp_pc_it)) { exp_pc_xl_nts.insert(*exp_pc_it); }; + } + else + { + exp_pc_nucleotide_count[*exp_pc_it]++; + } + } + + // check if at least one nucleotide present that can cross link + bool has_xl_nt(false); + for (auto const & m : exp_pc_nucleotide_count) { if (can_xl.count(m.first)) { has_xl_nt = true; break; } } + + LOG_DEBUG << "\t" << exp_pc_adduct << " has cross-linkable nucleotide (0 = false, 1 = true): " << has_xl_nt << endl; + + // no cross-linkable nt contained in the precursor adduct? Return an empty fragment adduct definition set + if (!has_xl_nt) { return ret; } + + // HERE: at least one cross-linkable nt present in precursor adduct + + // extract loss string from precursor adduct (e.g.: "-H2O") + // String exp_pc_loss_string(exp_pc_it, exp_pc_adduct.end()); + + LOG_DEBUG << "\t" << exp_pc_adduct << " is monomer (1 = true, >1 = false): " << nt_count << endl; + + // Handle the cases of monomer or oligo nucleotide bound to the precursor. + // This distinction is made because potential losses on the precursor only allows us to reduce the set of chemical feasible fragment adducts if they are on a monomer. + // In the case of an oligo we can't be sure if the cross-linked amino acid or any other in the oligo had the loss. + if (nt_count > 1) // No monomer? For every nucleotide that can be cross-linked: Create all fragment adducts without restriction by losses (no restriction as the loss could be on the other nts) + { + // for each nucleotide and potential set of fragment adducts + for (auto const & n2fa : nucleotide_to_fragment_adducts) + { + const char & nucleotide = n2fa.first; // the nucleotide without any associated loss + const set& fragment_adducts = n2fa.second; // all potential fragment adducts that may arise from the unmodified nucleotide + + // check if nucleotide is cross-linkable and part of the precursor adduct + if (exp_pc_xl_nts.find(nucleotide) != exp_pc_xl_nts.end()) + { + LOG_DEBUG << "\t" << exp_pc_adduct << " found nucleotide: " << String(nucleotide) << " in precursor RNA." << endl; + LOG_DEBUG << "\t" << exp_pc_adduct << " nucleotide: " << String(nucleotide) << " has fragment_adducts: " << fragment_adducts.size() << endl; + + // store feasible adducts associated with a cross-link with character nucleotide + vector faa; + std::copy(fragment_adducts.begin(), fragment_adducts.end(), back_inserter(faa)); + ret.feasible_adducts.emplace_back(make_pair(nucleotide, faa)); + } + } + + // Create set of marker ions for all nucleotides contained in the precursor (including those that do not cross-link.) + // Note: The non-cross-linked nt in the precursor adduct are more likely to produce the marker ions (=more fragile than the cross-linked nt). + set marker_ion_set; + for (auto const & n2fa : nucleotide_to_fragment_adducts) + { + const char & nucleotide = n2fa.first; // the nucleotide without any associated loss + if (exp_pc_nucleotide_count.find(nucleotide) != exp_pc_nucleotide_count.end()) { marker_ion_set.insert(n2fa.second.begin(), n2fa.second.end()); } + } + std::move(std::begin(marker_ion_set), std::end(marker_ion_set), std::back_inserter(ret.marker_ions)); + } + else // nt_count == 1: monomer. We need to check if the neutral loss reduces the set of feasible (e.g., chemically sound) fragment adducts + { + for (auto const & n2fa : nucleotide_to_fragment_adducts) + { + const char & nucleotide = n2fa.first; // one letter code of the nt + set fas = n2fa.second; // all potential fragment adducts that may arise from nt (if no losses are considered) + + // check if nucleotide is cross-linkable and part of the precursor adduct + if (exp_pc_xl_nts.find(nucleotide) != exp_pc_xl_nts.end()) + { + LOG_DEBUG << "\t" << exp_pc_adduct << " found nucleotide: " << String(nucleotide) << " in precursor RNA." << endl; + LOG_DEBUG << "\t" << exp_pc_adduct << " nucleotide: " << String(nucleotide) << " has fragment_adducts: " << fas.size() << endl; + + // check chemical feasibility by checking if subtraction of adduct would result in negative elemental composition + for (auto it = fas.begin(); it != fas.end(); ) + { + bool negative_elements = (EmpiricalFormula(exp_pc_formula) - it->formula).toString().hasSubstring("-"); + + if (negative_elements) // fragment adduct can't be subformula of precursor adduct + { + it = fas.erase(it); + } + else + { + ++it; // STL erase idiom (mind the pre-increment) + } + } + + // store feasible adducts associated with a cross-link with character nucleotide[0] + vector faa; + std::copy(fas.begin(), fas.end(), back_inserter(faa)); + ret.feasible_adducts.emplace_back(make_pair(nucleotide, faa)); + + // store feasible marker ions (in this case (monomer) we also restrict them on the nt on the precursor) + // Note that these peaks are likely missing or of very low intensity, + std::copy(std::begin(fas), std::end(fas), std::back_inserter(ret.marker_ions)); + } + } + } + + // Because, e.g., ribose might be a feasible fragment of any nucleotide, we keep only one version + // Note: sort by formula and (as tie breaker) the name + std::sort(ret.marker_ions.begin(), ret.marker_ions.end(), + [](RNPxlFragmentAdductDefinition const & a, RNPxlFragmentAdductDefinition const & b) + { + const String as = a.formula.toString(); + const String bs = b.formula.toString(); + return std::tie(as, a.name) < std::tie(bs, b.name); + } + ); + // Note: for uniqueness, we only rely on the formula (in case of tie: keeping the first = shortest name) + auto it = std::unique(ret.marker_ions.begin(), ret.marker_ions.end(), + [](RNPxlFragmentAdductDefinition const & a, RNPxlFragmentAdductDefinition const & b) + { + return a.formula == b.formula; + } + ); + ret.marker_ions.resize(std::distance(ret.marker_ions.begin(), it)); + + // print feasible fragment adducts + for (auto const & ffa : ret.feasible_adducts) + { + const char & nucleotide = ffa.first; + LOG_DEBUG << " Cross-linkable nucleotide '" << nucleotide << "' and feasible fragment adducts:" << endl; + for (auto const & a : ffa.second) + { + LOG_DEBUG << "\t" << a.name << "\t" << a.formula.toString() << "\t" << a.mass << "\n"; + } + } + + // print marker ions + LOG_DEBUG << " Marker ions:" << endl; + for (auto const & a : ret.marker_ions) + { + LOG_DEBUG << "\t" << a.name << "\t" << a.formula.toString() << "\t" << a.mass << "\n"; + } + + return ret; +} + + +vector RNPxlParameterParsing::getModifications(StringList modNames) +{ + vector modifications; + + // iterate over modification names and add to vector + for (String modification : modNames) + { + ResidueModification rm; + if (modification.hasSubstring(" (N-term)")) + { + modification.substitute(" (N-term)", ""); + rm = *ModificationsDB::getInstance()->getModification(modification, "", ResidueModification::N_TERM); + } + else if (modification.hasSubstring(" (C-term)")) + { + modification.substitute(" (C-term)", ""); + rm = *ModificationsDB::getInstance()->getModification(modification, "", ResidueModification::C_TERM); + } + else + { + rm = *ModificationsDB::getInstance()->getModification(modification); + } + modifications.push_back(rm); + } + + return modifications; +} + + +} + diff --git a/src/openms/source/ANALYSIS/RNPXL/sources.cmake b/src/openms/source/ANALYSIS/RNPXL/sources.cmake index 091c3d5751b..1975ac87f5a 100644 --- a/src/openms/source/ANALYSIS/RNPXL/sources.cmake +++ b/src/openms/source/ANALYSIS/RNPXL/sources.cmake @@ -7,9 +7,12 @@ HyperScore.cpp ModifiedPeptideGenerator.cpp MorpheusScore.cpp PScore.cpp +RNPxlFragmentAdductDefinition.cpp RNPxlFragmentAnnotationHelper.cpp +RNPxlFragmentIonGenerator.cpp RNPxlMarkerIonExtractor.cpp RNPxlModificationsGenerator.cpp +RNPxlParameterParsing.cpp RNPxlReport.cpp ) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index da19e0abc0a..2d52bd50b05 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -55,6 +55,8 @@ #include #include #include +#include +#include #include #include @@ -134,82 +136,6 @@ struct ImmoniumIonsInPeptide bool M = false; }; -struct RNPxlFragmentAdductDefinition -{ - EmpiricalFormula formula; // formula - String name; // name used in annotation - double mass = 0; - - RNPxlFragmentAdductDefinition() = default; - - RNPxlFragmentAdductDefinition(const RNPxlFragmentAdductDefinition&) = default; - - RNPxlFragmentAdductDefinition(RNPxlFragmentAdductDefinition&&) = default; - - RNPxlFragmentAdductDefinition& operator=(const RNPxlFragmentAdductDefinition&) = default; - - RNPxlFragmentAdductDefinition& operator=(RNPxlFragmentAdductDefinition&&) = default; - - bool operator<(const RNPxlFragmentAdductDefinition& other) const - { - String fa = formula.toString(); - String fb = other.formula.toString(); - return std::tie(mass, fa, name) < std::tie(other.mass, fb, other.name); - } - - bool operator==(const RNPxlFragmentAdductDefinition& other) const - { - return std::tie(formula, name) == std::tie(other.formula, other.name); - } - -}; - -// fast (flat) data structure to store feasible x-,y-,a-ion fragment adducts and observable marker ions -using NucleotideToFeasibleFragmentAdducts = pair >; - -// stores the fragment adducts and marker ions for a given precursor adduct -struct MS2AdductsOfSinglePrecursorAdduct -{ - vector feasible_adducts; - vector marker_ions; -}; - -// helper struct to facilitate parsing of parameters (modifications, nucleotide adducts, ...) -struct RNPxlParameterParsing -{ - /// Query ResidueModifications (given as strings) from ModificationsDB - static vector getModifications(StringList modNames); - - // Map a nucleotide (e.g. U to all possible fragment adducts) - using NucleotideToFragmentAdductMap = map >; - // @brief Parse tool parameter to create map from target nucleotide to all its fragment adducts - // It maps a single letter nucleotide (e.g., 'T', 'C', ...) - // to the maximum set of fragment adducts that may arise if the nucleotide is cross-linked. - // Losses, that might reduce this set, are not considered in this data structure and handled later - // when specific precursor adducts are considered. - static NucleotideToFragmentAdductMap getTargetNucleotideToFragmentAdducts(StringList fragment_adducts); - - // @brief Determines the fragment adducts and marker ions for a given precursor. - // The precursor adduct (the oligo including losses, e.g.: "TC-H3PO4") is mapped to all contained nucleotides - // and their marker ions. In addition, each cross-linkable nucleotide is mapped to its chemically feasible fragment adducts. - // Chemical feasible means in this context, that the fragment or marker ion adduct is a subformula of the precursor adduct. - static MS2AdductsOfSinglePrecursorAdduct getFeasibleFragmentAdducts( - const String& exp_pc_adduct, - const String& exp_pc_formula, - const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, - const set& can_xl - ); - - // Maps a precursor adduct (e.g.: "UU-H2O") to all chemically feasible fragment adducts. - using PrecursorsToMS2Adducts = map; - - // @brief Calculate all chemically feasible fragment adducts for all possible precursor adducts - // Same as getFeasibleFragmentAdducts but calculated from all precursor adducts - static PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts( - const RNPxlModificationMassesResult& precursor_adducts, - const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, - const set& can_xl); -}; /// Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space /// floats need to be initialized to zero as default @@ -217,8 +143,8 @@ class AnnotatedHit { public: StringView sequence; - SignedSize peptide_mod_index = 0; // enumeration index of the non-RNA peptide modification - Size rna_mod_index = 0; // index of the RNA modification + SignedSize peptide_mod_index = 0; // enumeration index of the non-NA peptide modification + Size rna_mod_index = 0; // index of the NA modification int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment float mass_error_p = 0; @@ -265,52 +191,6 @@ class AnnotatedHit } }; -// helper class that adds special ions not covered by TheoreticalSpectrumGenerator -class RNPxlFragmentIonGenerator -{ - public: - // prefix used to denote marker ions in fragment annotations - static constexpr const char* ANNOTATIONS_MARKER_ION_PREFIX = "MI:"; - - // add RNA-marker ions of charge 1 - // this includes the protonated nitrogenous base and all shifts (e.g., U-H2O, U'-H20, ...) - static void addMS2MarkerIons( - const vector& marker_ions, - PeakSpectrum& spectrum, - PeakSpectrum::IntegerDataArray& spectrum_charge, - PeakSpectrum::StringDataArray& spectrum_annotation); - - static void addShiftedImmoniumIons( - const String & unmodified_sequence, - const String & fragment_shift_name, - const double fragment_shift_mass, - PeakSpectrum & partial_loss_spectrum, - PeakSpectrum::IntegerDataArray& partial_loss_spectrum_charge, - PeakSpectrum::StringDataArray& partial_loss_spectrum_annotation); - - static void generatePartialLossSpectrum(const String& unmodified_sequence, - const double& fixed_and_variable_modified_peptide_weight, - const String& precursor_rna_adduct, - const double& precursor_rna_mass, - const int& precursor_charge, - const vector& partial_loss_modification, - const PeakSpectrum& patial_loss_template_z1, - const PeakSpectrum& patial_loss_template_z2, - const PeakSpectrum& patial_loss_template_z3, - PeakSpectrum& partial_loss_spectrum); - static void addPrecursorWithCompleteRNA_(const double fixed_and_variable_modified_peptide_weight, - const String & precursor_rna_adduct, - const double precursor_rna_mass, - const int charge, - PeakSpectrum & partial_loss_spectrum, - MSSpectrum::IntegerDataArray & partial_loss_spectrum_charge, - MSSpectrum::StringDataArray & partial_loss_spectrum_annotation); - - static void addSpecialLysImmonumIons(const String& unmodified_sequence, - PeakSpectrum &spectrum, - PeakSpectrum::IntegerDataArray &spectrum_charge, - PeakSpectrum::StringDataArray &spectrum_annotation); -}; class RNPxlSearch : public TOPPBase @@ -398,7 +278,7 @@ class RNPxlSearch : // RNPxl specific registerTOPPSubsection_("RNPxl", "RNPxl Options"); - registerIntOption_("RNPxl:length", "", 2, "Oligonucleotide maximum length. 0 = disable search for RNA variants.", false); + registerIntOption_("RNPxl:length", "", 2, "Oligonucleotide maximum length. 0 = disable search for NA variants.", false); registerStringOption_("RNPxl:sequence", "", "", "Sequence to restrict the generation of oligonucleotide chains. (disabled for empty sequence)", false); @@ -1089,7 +969,7 @@ static void scoreShiftedFragments_( // for each PSM of this spectrum for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) { - // determine RNA on precursor from index in map + // determine NA on precursor from index in map auto mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, annotated_hits[scan_index][i].rna_mod_index); const String precursor_rna_adduct = *mod_combinations_it->second.begin(); @@ -1121,16 +1001,16 @@ static void scoreShiftedFragments_( { AnnotatedHit& ah = annotated_hits[scan_index][i]; - // reconstruct fixed and variable modified peptide sequence (without RNA) + // reconstruct fixed and variable modified peptide sequence (without NA) const String& unmodified_sequence = ah.sequence.getString(); AASequence aas = AASequence::fromString(unmodified_sequence); vector all_modified_peptides; ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications.begin(), fixed_modifications.end(), aas); ModifiedPeptideGenerator::applyVariableModifications(variable_modifications.begin(), variable_modifications.end(), aas, max_variable_mods_per_peptide, all_modified_peptides); AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; - double current_peptide_mass_without_RNA = fixed_and_variable_modified_peptide.getMonoWeight(); + double current_peptide_mass_without_NA = fixed_and_variable_modified_peptide.getMonoWeight(); - // determine RNA on precursor from index in map + // determine NA on precursor from index in map auto mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, ah.rna_mod_index); const String precursor_rna_adduct = *mod_combinations_it->second.begin(); @@ -1175,7 +1055,7 @@ static void scoreShiftedFragments_( // shifted b- / y- / a-ions // generate shifted_immonium_ions_sub_score_spectrum.empty RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - current_peptide_mass_without_RNA, + current_peptide_mass_without_NA, precursor_rna_adduct, precursor_rna_mass, 1, @@ -1186,7 +1066,7 @@ static void scoreShiftedFragments_( partial_loss_spectrum_z1); RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - current_peptide_mass_without_RNA, + current_peptide_mass_without_NA, precursor_rna_adduct, precursor_rna_mass, 2, // don't know the charge of the precursor at that point @@ -1275,7 +1155,7 @@ static void scoreShiftedFragments_( const AASequence& fixed_and_variable_modified_peptide = all_modified_peptides[a.peptide_mod_index]; const double fixed_and_variable_modified_peptide_weight = fixed_and_variable_modified_peptide.getMonoWeight(); - // determine RNA on precursor from index in map + // determine NA on precursor from index in map std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, a.rna_mod_index); const String precursor_rna_adduct = *mod_combinations_it->second.begin(); @@ -1285,7 +1165,7 @@ static void scoreShiftedFragments_( if (precursor_rna_adduct == "none") { continue; } // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum - // 1. get all possible RNA fragment shifts in the MS2 (based on the precursor RNA/DNA) + // 1. get all possible NA fragment shifts in the MS2 (based on the precursor RNA/DNA) LOG_DEBUG << "Precursor NA adduct: " << precursor_rna_adduct << endl; const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; @@ -1310,7 +1190,7 @@ static void scoreShiftedFragments_( LOG_DEBUG << fa.name << " " << fa.mass << endl; } - // generate total loss spectrum for the fixed and variable modified peptide (without RNA) (using the settings for partial loss generation) + // generate total loss spectrum for the fixed and variable modified peptide (without NAs) (using the settings for partial loss generation) // but as we also add the abundant immonium ions for charge 1 and precursor ions for all charges to get a more complete annotation // (these have previously not been used in the scoring of the total loss spectrum) PeakSpectrum total_loss_spectrum; @@ -1935,7 +1815,7 @@ static void scoreShiftedFragments_( ph.setScore(ah.score); ph.setMetaValue(String("RNPxl:score"), ah.score); // important for Percolator feature set because the PeptideHit score might be overwritten by a q-value - // determine RNA modification from index in map + // determine NA modification from index in map std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, ah.rna_mod_index); ph.setMetaValue(String("RNPxl:mass_error_p"), ah.mass_error_p); @@ -1962,7 +1842,7 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("RNPxl:RNA"), *mod_combinations_it->second.begin()); // return first nucleotide formula matching the index of the empirical formula ph.setMetaValue(String("RNPxl:NT"), String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide - ph.setMetaValue(String("RNPxl:RNA_MASS_z0"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight()); // RNA uncharged mass via empirical formula + ph.setMetaValue(String("RNPxl:RNA_MASS_z0"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight()); // NA uncharged mass via empirical formula ph.setMetaValue(String("RNPxl:best_localization_score"), ah.best_localization_score); ph.setMetaValue(String("RNPxl:localization_scores"), ah.localization_scores); @@ -2275,7 +2155,7 @@ static void scoreShiftedFragments_( if (!getFlag_("RNPxl:only_xl")) { - mm.mod_masses[""] = 0; // insert "null" modification otherwise peptides without RNA will not be searched + mm.mod_masses[""] = 0; // insert "null" modification otherwise peptides without NA will not be searched mm.mod_combinations[""].insert("none"); } @@ -2480,7 +2360,7 @@ static void scoreShiftedFragments_( for (SignedSize mod_pep_idx = 0; mod_pep_idx < (SignedSize)all_modified_peptides.size(); ++mod_pep_idx) { const AASequence& fixed_and_variable_modified_peptide = all_modified_peptides[mod_pep_idx]; - double current_peptide_mass_without_RNA = fixed_and_variable_modified_peptide.getMonoWeight(); + double current_peptide_mass_without_NA = fixed_and_variable_modified_peptide.getMonoWeight(); //create empty theoretical spectrum. total_loss_spectrum_z2 contains both charge 1 and charge 2 peaks PeakSpectrum total_loss_spectrum_z1, total_loss_spectrum_z2; @@ -2491,7 +2371,7 @@ static void scoreShiftedFragments_( precursor_sub_score_spectrum, marker_ions_sub_score_spectrum; - // iterate over all RNA sequences, calculate peptide mass and generate complete loss spectrum only once as this can potentially be reused + // iterate over all NA sequences, calculate peptide mass and generate complete loss spectrum only once as this can potentially be reused Size rna_mod_index = 0; // TODO: track the XL-able nt here @@ -2500,7 +2380,7 @@ static void scoreShiftedFragments_( ++rna_mod_it, ++rna_mod_index) { const double precursor_rna_mass = rna_mod_it->second; - const double current_peptide_mass = current_peptide_mass_without_RNA + precursor_rna_mass; // add RNA mass + const double current_peptide_mass = current_peptide_mass_without_NA + precursor_rna_mass; // add NA mass // TODO: const char xl_nucleotide; // can be none // determine MS2 precursors that match to the current peptide mass @@ -2543,14 +2423,14 @@ static void scoreShiftedFragments_( if (!fast_scoring_) { - // retrieve RNA adduct name + // retrieve NA adduct name auto mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, rna_mod_index); const String& precursor_rna_adduct = *mod_combinations_it->second.begin(); if (precursor_rna_adduct == "none") { - // score peptide without RNA (same method as fast scoring) + // score peptide without NA (same method as fast scoring) for (auto l = low_it; l != up_it; ++l) { //const double exp_pc_mass = l->first; @@ -2641,10 +2521,10 @@ static void scoreShiftedFragments_( #endif } } - else // score peptide with RNA adduct + else // score peptide with NA MS1 adduct { // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum - // get RNA fragment shifts in the MS2 (based on the precursor RNA/DNA) + // get NA fragment shifts in the MS2 (based on the precursor RNA/DNA) auto const & all_NA_adducts = all_feasible_fragment_adducts.at(precursor_rna_adduct); const vector& feasible_MS2_adducts = all_NA_adducts.feasible_adducts; // get marker ions @@ -2655,7 +2535,7 @@ static void scoreShiftedFragments_( // String("FATAL: No feasible adducts for " + precursor_rna_adduct).c_str()); - // Do we have (nucleotide) specific fragmentation adducts? for the current RNA adduct on the precursor? + // Do we have (nucleotide) specific fragmentation adducts? for the current NA adduct on the precursor? // If so, generate spectra for shifted ion series @@ -2677,7 +2557,7 @@ static void scoreShiftedFragments_( { // shifted b- / y- / a-ions RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - current_peptide_mass_without_RNA, + current_peptide_mass_without_NA, precursor_rna_adduct, precursor_rna_mass, 1, @@ -2688,7 +2568,7 @@ static void scoreShiftedFragments_( partial_loss_spectrum_z1); RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - current_peptide_mass_without_RNA, + current_peptide_mass_without_NA, precursor_rna_adduct, precursor_rna_mass, 2, // don't know the charge of the precursor at that point @@ -2772,7 +2652,7 @@ static void scoreShiftedFragments_( unmodified_sequence.size(), iip, exp_spectrum, - current_peptide_mass_without_RNA, + current_peptide_mass_without_NA, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, partial_loss_template_z1_bions, @@ -3236,683 +3116,6 @@ static void scoreShiftedFragments_( } }; -vector RNPxlParameterParsing::getModifications(StringList modNames) -{ - vector modifications; - - // iterate over modification names and add to vector - for (String modification : modNames) - { - ResidueModification rm; - if (modification.hasSubstring(" (N-term)")) - { - modification.substitute(" (N-term)", ""); - rm = *ModificationsDB::getInstance()->getModification(modification, "", ResidueModification::N_TERM); - } - else if (modification.hasSubstring(" (C-term)")) - { - modification.substitute(" (C-term)", ""); - rm = *ModificationsDB::getInstance()->getModification(modification, "", ResidueModification::C_TERM); - } - else - { - rm = *ModificationsDB::getInstance()->getModification(modification); - } - modifications.push_back(rm); - } - - return modifications; -} - -RNPxlParameterParsing::PrecursorsToMS2Adducts -RNPxlParameterParsing::getAllFeasibleFragmentAdducts( - const RNPxlModificationMassesResult & precursor_adducts, - const RNPxlParameterParsing::NucleotideToFragmentAdductMap & nucleotide_to_fragment_adducts, - const set & can_xl) -{ - PrecursorsToMS2Adducts all_pc_all_feasible_adducts; - - map pc2mass; - map pc2ef; - - using PrecursorAdductMassAndMS2Fragments = pair>; - using PrecursorAdductAndXLNucleotide = pair; - map> mass_frags2pc_xlnuc; - - // for all distinct precursor adduct formulas/masses - for (auto const & pa : precursor_adducts.mod_masses) - { - // get all precursor nucleotide formulas matching current empirical formula/mass - const String& ef = pa.first; - const double pc_mass = pa.second; - const set& ambiguities = precursor_adducts.mod_combinations.at(ef); - - if (ambiguities.size() >= 2) - { - LOG_DEBUG << ambiguities.size() << " nucleotide formulas are ambiguous on the level of empirical formula: " << endl; - for (auto const & pc_adduct : ambiguities) { LOG_DEBUG << pc_adduct << endl; } - } - - // for each ambiguous (at the level of empirical formula) precursor adduct (stored as nucleotide formula e.g.: "AU-H2O") - for (const String & pc_adduct : ambiguities) - { - // calculate feasible fragment adducts and store them for lookup - const MS2AdductsOfSinglePrecursorAdduct& feasible_adducts = getFeasibleFragmentAdducts(pc_adduct, ef, nucleotide_to_fragment_adducts, can_xl); - // TODO: check if needed anymore - std::sort(feasible_adducts.begin(), feasible_adducts.end()); - all_pc_all_feasible_adducts[pc_adduct] = feasible_adducts; - pc2mass[pc_adduct] = pc_mass; - pc2ef[pc_adduct] = ef; - } - } - - // print feasible fragment adducts and marker ions - for (auto const & fa : all_pc_all_feasible_adducts) - { - const String & pc = fa.first; - LOG_DEBUG << "Precursor adduct: " << pc << "\t" << pc2ef[pc] << "\t" << pc2mass[pc] << "\n"; - - // collect set of masses to detect ambiguities - set mi_fragments; - for (auto const & mis : fa.second.marker_ions) { mi_fragments.insert(mis.mass); } - - for (auto const & ffa : fa.second.feasible_adducts) - { - const char & nucleotide = ffa.first; - set fragments; - for (auto const & f : mi_fragments) { fragments.insert(f); } // copy over common marker ion masses - for (auto const & f : ffa.second) { fragments.insert(f.mass); } // copy over xl-ed nucleotide associated fragment masses - // we want to track if a certain MS1 mass and set of MS2 ions allow to distinguish - // (at least in theory) precursor adduct and cross-linked nucleotide - // to do so, we map mass and set of fragment ions to precursor adduct and cross-linked nucleotide - mass_frags2pc_xlnuc[{pc2mass[pc], fragments}].push_back({pc, nucleotide}); - - LOG_DEBUG << " Cross-linkable nucleotide '" << nucleotide << "' and feasible fragment adducts:" << endl; - for (auto const & a : ffa.second) - { - LOG_DEBUG << " " << a.name << "\t" << a.formula.toString() << "\t" << a.mass << "\n"; - } - } - - LOG_DEBUG << " Marker ions." << endl; - for (auto const & ffa : fa.second.marker_ions) - { - LOG_DEBUG << " " << ffa.name << "\t" << ffa.formula.toString() << "\t" << ffa.mass << "\n"; - } - } - LOG_DEBUG << endl; - - // report precursor adducts/cross-linked nucleotide combinations with same mass that produce the exact same MS2 ions as indistinguishable - for (auto const & f : mass_frags2pc_xlnuc) - { - if (f.second.size() > 1) - { - LOG_INFO << "Theoretical indistinguishable cross-links detected: " << endl; - for (auto const & m : f.second) - { - LOG_INFO << "Precursor: " << m.first << "\t and cross-linked nucleotide: " << m.second << endl; - for (auto const & fragment_mass : f.first.second) - { - LOG_INFO << "Fragment mass: " << fragment_mass << endl; - } - } - } - } - - return all_pc_all_feasible_adducts; -} - -RNPxlParameterParsing::NucleotideToFragmentAdductMap -RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringList fragment_adducts) -{ - NucleotideToFragmentAdductMap nucleotide_to_fragment_adducts; - for (String t : fragment_adducts) - { - t.removeWhitespaces(); - - EmpiricalFormula formula; - String name; - - // format is: target_nucletide:formula;name - char target_nucleotide = t[0]; - if (t[1] != ':') - { - LOG_WARN << "Missing ':'. Wrong format of fragment_adduct string: " << t << endl; - return NucleotideToFragmentAdductMap(); - } - - // remove target nucleotide and : character from t - t = t.substr(2); - - // split into formula and name - vector fs; - t.split(";", fs); - if (fs.size() == 1) // no name provided so we just take the formula as name - { - formula = EmpiricalFormula(fs[0]); - name = formula.toString(); - } - else if (fs.size() == 2) - { - formula = EmpiricalFormula(fs[0]); - name = fs[1]; - } - else - { - LOG_WARN << "Wrong format of fragment_adduct string: " << t << endl; - return NucleotideToFragmentAdductMap(); - } - - RNPxlFragmentAdductDefinition fad; - fad.name = name; - fad.formula = formula; - fad.mass = formula.getMonoWeight(); - - nucleotide_to_fragment_adducts[target_nucleotide].insert(fad); - - // register all fragment adducts as N- and C-terminal modification (if not already registered) - if (!ModificationsDB::getInstance()->has(name)) - { - ResidueModification * c_term = new ResidueModification(); - c_term->setId(name); - c_term->setName(name); - c_term->setFullId(name + " (C-term)"); - c_term->setTermSpecificity(ResidueModification::C_TERM); - c_term->setDiffMonoMass(fad.mass); - ModificationsDB::getInstance()->addModification(c_term); - - ResidueModification * n_term = new ResidueModification(); - n_term->setId(name); - n_term->setName(name); - n_term->setFullId(name + " (N-term)"); - n_term->setTermSpecificity(ResidueModification::N_TERM); - n_term->setDiffMonoMass(fad.mass); - ModificationsDB::getInstance()->addModification(n_term); - } - } - -#ifdef DEBUG_RNPXLSEARCH - for (auto const & p2fas : precursor_to_fragment_adducts) - { - for (auto const & p2fa : p2fas.second) - { - cout << "nucleotide:" << p2fas.first - << " fragment adduct:" << p2fa.formula.toString() - << " fragment adduct mass:" << p2fa.mass - << " name:" << p2fa.name << endl; - } - } -#endif - - return nucleotide_to_fragment_adducts; -} - -MS2AdductsOfSinglePrecursorAdduct -RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, - const String &exp_pc_formula, - const RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, - const set &can_xl) -{ - LOG_DEBUG << "Generating fragment adducts for precursor adduct: '" << exp_pc_adduct << "'" << endl; - - MS2AdductsOfSinglePrecursorAdduct ret; - - // no precursor adduct? - if (exp_pc_formula.empty()) { return ret; } // no fragment adducts or marker ions are expected! - - // count nucleotides in precursor adduct (e.g.: "TCA-H2O" yields map: T->1, C->1, A->1) - // and determine the set of cross-linkable nucleotides in the precursor adduct - size_t nt_count(0); - map exp_pc_nucleotide_count; - set exp_pc_xl_nts; - String::const_iterator exp_pc_it = exp_pc_adduct.begin(); - for (; exp_pc_it != exp_pc_adduct.end(); ++exp_pc_it, ++nt_count) - { - // we are finished with nucleotides in string if first loss/gain is encountered - if (*exp_pc_it == '+' || *exp_pc_it == '-') break; - - // count occurence of nucleotide - if (exp_pc_nucleotide_count.count(*exp_pc_it) == 0) - { - exp_pc_nucleotide_count[*exp_pc_it] = 1; - if (can_xl.count(*exp_pc_it)) { exp_pc_xl_nts.insert(*exp_pc_it); }; - } - else - { - exp_pc_nucleotide_count[*exp_pc_it]++; - } - } - - // check if at least one nucleotide present that can cross link - bool has_xl_nt(false); - for (auto const & m : exp_pc_nucleotide_count) { if (can_xl.count(m.first)) { has_xl_nt = true; break; } } - - LOG_DEBUG << "\t" << exp_pc_adduct << " has cross-linkable nucleotide (0 = false, 1 = true): " << has_xl_nt << endl; - - // no cross-linkable nt contained in the precursor adduct? Return an empty fragment adduct definition set - if (!has_xl_nt) { return ret; } - - // HERE: at least one cross-linkable nt present in precursor adduct - - // extract loss string from precursor adduct (e.g.: "-H2O") - // String exp_pc_loss_string(exp_pc_it, exp_pc_adduct.end()); - - LOG_DEBUG << "\t" << exp_pc_adduct << " is monomer (1 = true, >1 = false): " << nt_count << endl; - - // Handle the cases of monomer or oligo nucleotide bound to the precursor. - // This distinction is made because potential losses on the precursor only allows us to reduce the set of chemical feasible fragment adducts if they are on a monomer. - // In the case of an oligo we can't be sure if the cross-linked amino acid or any other in the oligo had the loss. - if (nt_count > 1) // No monomer? For every nucleotide that can be cross-linked: Create all fragment adducts without restriction by losses (no restriction as the loss could be on the other nts) - { - // for each nucleotide and potential set of fragment adducts - for (auto const & n2fa : nucleotide_to_fragment_adducts) - { - const char & nucleotide = n2fa.first; // the nucleotide without any associated loss - const set& fragment_adducts = n2fa.second; // all potential fragment adducts that may arise from the unmodified nucleotide - - // check if nucleotide is cross-linkable and part of the precursor adduct - if (exp_pc_xl_nts.find(nucleotide) != exp_pc_xl_nts.end()) - { - LOG_DEBUG << "\t" << exp_pc_adduct << " found nucleotide: " << String(nucleotide) << " in precursor RNA." << endl; - LOG_DEBUG << "\t" << exp_pc_adduct << " nucleotide: " << String(nucleotide) << " has fragment_adducts: " << fragment_adducts.size() << endl; - - // store feasible adducts associated with a cross-link with character nucleotide - vector faa; - std::copy(fragment_adducts.begin(), fragment_adducts.end(), back_inserter(faa)); - ret.feasible_adducts.emplace_back(make_pair(nucleotide, faa)); - } - } - - // Create set of marker ions for all nucleotides contained in the precursor (including those that do not cross-link.) - // Note: The non-cross-linked nt in the precursor adduct are more likely to produce the marker ions (=more fragile than the cross-linked nt). - set marker_ion_set; - for (auto const & n2fa : nucleotide_to_fragment_adducts) - { - const char & nucleotide = n2fa.first; // the nucleotide without any associated loss - if (exp_pc_nucleotide_count.find(nucleotide) != exp_pc_nucleotide_count.end()) { marker_ion_set.insert(n2fa.second.begin(), n2fa.second.end()); } - } - std::move(std::begin(marker_ion_set), std::end(marker_ion_set), std::back_inserter(ret.marker_ions)); - } - else // nt_count == 1: monomer. We need to check if the neutral loss reduces the set of feasible (e.g., chemically sound) fragment adducts - { - for (auto const & n2fa : nucleotide_to_fragment_adducts) - { - const char & nucleotide = n2fa.first; // one letter code of the nt - set fas = n2fa.second; // all potential fragment adducts that may arise from nt (if no losses are considered) - - // check if nucleotide is cross-linkable and part of the precursor adduct - if (exp_pc_xl_nts.find(nucleotide) != exp_pc_xl_nts.end()) - { - LOG_DEBUG << "\t" << exp_pc_adduct << " found nucleotide: " << String(nucleotide) << " in precursor RNA." << endl; - LOG_DEBUG << "\t" << exp_pc_adduct << " nucleotide: " << String(nucleotide) << " has fragment_adducts: " << fas.size() << endl; - - // check chemical feasibility by checking if subtraction of adduct would result in negative elemental composition - for (auto it = fas.begin(); it != fas.end(); ) - { - bool negative_elements = (EmpiricalFormula(exp_pc_formula) - it->formula).toString().hasSubstring("-"); - - if (negative_elements) // fragment adduct can't be subformula of precursor adduct - { - it = fas.erase(it); - } - else - { - ++it; // STL erase idiom (mind the pre-increment) - } - } - - // store feasible adducts associated with a cross-link with character nucleotide[0] - vector faa; - std::copy(fas.begin(), fas.end(), back_inserter(faa)); - ret.feasible_adducts.emplace_back(make_pair(nucleotide, faa)); - - // store feasible marker ions (in this case (monomer) we also restrict them on the nt on the precursor) - // Note that these peaks are likely missing or of very low intensity, - std::copy(std::begin(fas), std::end(fas), std::back_inserter(ret.marker_ions)); - } - } - } - - // Because, e.g., ribose might be a feasible fragment of any nucleotide, we keep only one version - // Note: sort by formula and (as tie breaker) the name - std::sort(ret.marker_ions.begin(), ret.marker_ions.end(), - [](RNPxlFragmentAdductDefinition const & a, RNPxlFragmentAdductDefinition const & b) - { - const String as = a.formula.toString(); - const String bs = b.formula.toString(); - return std::tie(as, a.name) < std::tie(bs, b.name); - } - ); - // Note: for uniqueness, we only rely on the formula (in case of tie: keeping the first = shortest name) - auto it = std::unique(ret.marker_ions.begin(), ret.marker_ions.end(), - [](RNPxlFragmentAdductDefinition const & a, RNPxlFragmentAdductDefinition const & b) - { - return a.formula == b.formula; - } - ); - ret.marker_ions.resize(std::distance(ret.marker_ions.begin(), it)); - - // print feasible fragment adducts - for (auto const & ffa : ret.feasible_adducts) - { - const char & nucleotide = ffa.first; - LOG_DEBUG << " Cross-linkable nucleotide '" << nucleotide << "' and feasible fragment adducts:" << endl; - for (auto const & a : ffa.second) - { - LOG_DEBUG << "\t" << a.name << "\t" << a.formula.toString() << "\t" << a.mass << "\n"; - } - } - - // print marker ions - LOG_DEBUG << " Marker ions:" << endl; - for (auto const & a : ret.marker_ions) - { - LOG_DEBUG << "\t" << a.name << "\t" << a.formula.toString() << "\t" << a.mass << "\n"; - } - - return ret; -} - -void RNPxlFragmentIonGenerator::addMS2MarkerIons( - const vector &marker_ions, - PeakSpectrum &spectrum, - PeakSpectrum::IntegerDataArray &spectrum_charge, - PeakSpectrum::StringDataArray &spectrum_annotation) -{ - for (auto const & m : marker_ions) - { - const double mz = m.mass + Constants::PROTON_MASS_U; - - spectrum.emplace_back(mz, 1.0); - spectrum_charge.emplace_back(1); - spectrum_annotation.emplace_back(RNPxlFragmentIonGenerator::ANNOTATIONS_MARKER_ION_PREFIX + m.name); // add name (e.g., MI:U-H2O) - } -} - -void RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( - const String& unmodified_sequence, - PeakSpectrum &spectrum, - PeakSpectrum::IntegerDataArray &spectrum_charge, - PeakSpectrum::StringDataArray &spectrum_annotation) -{ - if (unmodified_sequence.has('K')) - { - const double immonium_ion2_mz = EmpiricalFormula("C5H10N1").getMonoWeight(); - // only add special ios if there is not already a peak - if (spectrum.findNearest(immonium_ion2_mz, 1e-4) == -1) - { - spectrum.emplace_back(immonium_ion2_mz, 1.0); - spectrum_charge.emplace_back(1); - spectrum_annotation.emplace_back(String("iK(C5H10N1)")); - } - - // usually only observed without shift (A. Stuetzer) - const double immonium_ion3_mz = EmpiricalFormula("C6H13N2O").getMonoWeight(); - // only add special ios if there is not already a peak - if (spectrum.findNearest(immonium_ion3_mz, 1e-4) == -1) - { - spectrum.emplace_back(immonium_ion3_mz, 1.0); - spectrum_charge.emplace_back(1); - spectrum_annotation.emplace_back(String("iK(C6H13N2O)")); - } - - } -} - - -void RNPxlFragmentIonGenerator::addShiftedImmoniumIons(const String &unmodified_sequence, - const String &fragment_shift_name, - const double fragment_shift_mass, - PeakSpectrum &partial_loss_spectrum, - PeakSpectrum::IntegerDataArray &partial_loss_spectrum_charge, - PeakSpectrum::StringDataArray &partial_loss_spectrum_annotation) -{ - if (unmodified_sequence.hasSubstring("Y")) - { - const double immonium_ion_mz = EmpiricalFormula("C8H10NO").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('Y', fragment_shift_name)); - } - else if (unmodified_sequence.hasSubstring("W")) - { - const double immonium_ion_mz = EmpiricalFormula("C10H11N2").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('W', fragment_shift_name)); - } - else if (unmodified_sequence.hasSubstring("F")) - { - const double immonium_ion_mz = EmpiricalFormula("C8H10N").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('F', fragment_shift_name)); - } - else if (unmodified_sequence.hasSubstring("H")) - { - const double immonium_ion_mz = EmpiricalFormula("C5H8N3").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('H', fragment_shift_name)); - } - else if (unmodified_sequence.hasSubstring("C")) - { - const double immonium_ion_mz = EmpiricalFormula("C2H6NS").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('C', fragment_shift_name)); - } - else if (unmodified_sequence.hasSubstring("P")) - { - const double immonium_ion_mz = EmpiricalFormula("C4H8N").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('P', fragment_shift_name)); - } - else if (unmodified_sequence.hasSubstring("L") || unmodified_sequence.hasSubstring("I")) - { - const double immonium_ion_mz = EmpiricalFormula("C5H12N").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('L', fragment_shift_name)); - } - else if (unmodified_sequence.hasSubstring("K")) - { - // classical immonium ion - const double immonium_ion_mz = EmpiricalFormula("C5H13N2").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('K', fragment_shift_name)); - - // TODO: check if only DNA specific and if also other shifts are observed - // according to A. Stuetzer mainly observed with C‘-NH3 (94.0167 Da) - const double immonium_ion2_mz = EmpiricalFormula("C5H10N1").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion2_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(String("iK(C5H10N1)" + fragment_shift_name)); - - // usually only observed without shift (A. Stuetzer) - const double immonium_ion3_mz = EmpiricalFormula("C6H13N2O").getMonoWeight() + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion3_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(String("iK(C6H13N2O)" + fragment_shift_name)); - } - else if (unmodified_sequence.hasSubstring("M")) - { - const double immonium_ion_mz = 104.05285 + fragment_shift_mass; - partial_loss_spectrum.emplace_back(immonium_ion_mz, 1.0); - partial_loss_spectrum_charge.emplace_back(1); - partial_loss_spectrum_annotation.emplace_back(RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon('M', fragment_shift_name)); - } -} - - /* - * Add peaks with shifts induced by the RNA/DNA: - * - Precursor with complete NA-oligo for charge 1..z - * - Partial shifts (without complete precursor adduct) - * - Add shifted immonium ions for charge 1 only - * and create shifted shifted b,y,a ions + precursors for charge 1..z (adding the unshifted version and performing the shift) - * based on the total_loss_spectrum provide to the method - */ -void RNPxlFragmentIonGenerator::generatePartialLossSpectrum(const String &unmodified_sequence, - const double &fixed_and_variable_modified_peptide_weight, - const String &precursor_rna_adduct, - const double &precursor_rna_mass, - const int &precursor_charge, - const vector &partial_loss_modification, - const PeakSpectrum& partial_loss_template_z1, - const PeakSpectrum& partial_loss_template_z2, - const PeakSpectrum& partial_loss_template_z3, - PeakSpectrum &partial_loss_spectrum) -{ - partial_loss_spectrum.getIntegerDataArrays().resize(1); - PeakSpectrum::IntegerDataArray& partial_loss_spectrum_charge = partial_loss_spectrum.getIntegerDataArrays()[0]; - - partial_loss_spectrum.getStringDataArrays().resize(1); // annotation - PeakSpectrum::StringDataArray& partial_loss_spectrum_annotation = partial_loss_spectrum.getStringDataArrays()[0]; - - // for all observable MS2 adducts ... - for (Size i = 0; i != partial_loss_modification.size(); ++i) - { - // get name and mass of fragment adduct - const String& fragment_shift_name = partial_loss_modification[i].name; // e.g. U-H2O - const double fragment_shift_mass = partial_loss_modification[i].mass; - - // ADD: shifted immonium ion peaks of charge 1 (if the amino acid is present in the sequence) - RNPxlFragmentIonGenerator::addShiftedImmoniumIons( - unmodified_sequence, - fragment_shift_name, - fragment_shift_mass, - partial_loss_spectrum, - partial_loss_spectrum_charge, - partial_loss_spectrum_annotation); - - // annotate generated a-,b-,y-ions with fragment shift name - PeakSpectrum shifted_series_peaks; - shifted_series_peaks.getStringDataArrays().resize(1); // annotation - shifted_series_peaks.getIntegerDataArrays().resize(1); // charge - - PeakSpectrum::StringDataArray& shifted_series_annotations = shifted_series_peaks.getStringDataArrays()[0]; - PeakSpectrum::IntegerDataArray& shifted_series_charges = shifted_series_peaks.getIntegerDataArrays()[0]; - - // For every charge state - for (int z = 1; z <= precursor_charge; ++z) - { - // 1. add shifted peaks - if (z == 1) - { - for (Size i = 0; i != partial_loss_template_z1.size(); ++i) - { - Peak1D p = partial_loss_template_z1[i]; - p.setMZ(p.getMZ() + fragment_shift_mass); - shifted_series_peaks.push_back(p); - shifted_series_annotations.push_back(partial_loss_template_z1.getStringDataArrays()[0][i]); - shifted_series_charges.push_back(1); - } - } - else if (z == 2) - { - for (Size i = 0; i != partial_loss_template_z2.size(); ++i) - { - // currently, also contains z=1 precursor peaks which we aleardy added before - if (partial_loss_template_z2.getIntegerDataArrays()[0][i] == 2) - { - Peak1D p = partial_loss_template_z2[i]; - p.setMZ(p.getMZ() + fragment_shift_mass / 2.0); - shifted_series_peaks.push_back(p); - shifted_series_annotations.push_back(partial_loss_template_z2.getStringDataArrays()[0][i]); - shifted_series_charges.push_back(2); - } - } - } - else if (z == 3) - { - for (Size i = 0; i != partial_loss_template_z3.size(); ++i) - { - // currently, also contains z=1 and 2 precursor peaks which we aleardy added before - if (partial_loss_template_z3.getIntegerDataArrays()[0][i] == 3) - { - Peak1D p = partial_loss_template_z3[i]; - p.setMZ(p.getMZ() + fragment_shift_mass / 3.0); - shifted_series_peaks.push_back(p); - shifted_series_annotations.push_back(partial_loss_template_z3.getStringDataArrays()[0][i]); - shifted_series_charges.push_back(3); - } - } - } - else // don't consider fragment ions with charge >= 4 - { - break; - } - } - - // 2. add fragment shift name to annotation of shifted peaks - for (Size j = 0; j != shifted_series_annotations.size(); ++j) - { - shifted_series_annotations[j] += " " + fragment_shift_name; - } - - // append shifted and annotated ion series to partial loss spectrum - partial_loss_spectrum.insert(partial_loss_spectrum.end(), - shifted_series_peaks.begin(), shifted_series_peaks.end()); - // std::move strings during insert - partial_loss_spectrum_annotation.insert( - partial_loss_spectrum_annotation.end(), - make_move_iterator(shifted_series_annotations.begin()), - make_move_iterator(shifted_series_annotations.end()) - ); - partial_loss_spectrum.getIntegerDataArrays()[0].insert( - partial_loss_spectrum_charge.end(), - shifted_series_charges.begin(), - shifted_series_charges.end() - ); - } - - // ADD: (mainly for ETD) MS2 precursor peaks of the MS1 adduct (total RNA) carrying peptide for all z <= precursor charge - for (int charge = 1; charge <= static_cast(precursor_charge); ++charge) - { - addPrecursorWithCompleteRNA_(fixed_and_variable_modified_peptide_weight, - precursor_rna_adduct, - precursor_rna_mass, - charge, - partial_loss_spectrum, - partial_loss_spectrum_charge, - partial_loss_spectrum_annotation); - } - - partial_loss_spectrum.sortByPosition(); -} - -void RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_( - const double fixed_and_variable_modified_peptide_weight, - const String &precursor_rna_adduct, - const double precursor_rna_mass, - const int charge, - PeakSpectrum &partial_loss_spectrum, - MSSpectrum::IntegerDataArray &partial_loss_spectrum_charge, - MSSpectrum::StringDataArray &partial_loss_spectrum_annotation) -{ - const double xl_mz = (fixed_and_variable_modified_peptide_weight + precursor_rna_mass + - static_cast(charge) * Constants::PROTON_MASS_U) - / static_cast(charge); - - // only add special ions if there is not already a peak - if (partial_loss_spectrum.findNearest(xl_mz, 1e-4) == -1) - { - partial_loss_spectrum.push_back(Peak1D(xl_mz, 1.0)); - partial_loss_spectrum_charge.push_back(charge); - if (charge > 1) - { - partial_loss_spectrum_annotation.push_back(String("[M+") - + String(charge) + "H+" + precursor_rna_adduct + "]"); - } - else - { - partial_loss_spectrum_annotation.push_back(String("[M+H+") - + precursor_rna_adduct + "]"); - } - } -} - int main(int argc, const char** argv) { RNPxlSearch tool; From e107ed19025155297bcf1e277cbc2fae1be07bb4 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 27 Mar 2019 12:50:05 +0100 Subject: [PATCH 027/471] [NOP] moved fast scoring to separate function --- src/utils/RNPxlSearch.cpp | 238 +++++++++++++++++++++++--------------- 1 file changed, 144 insertions(+), 94 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 2d52bd50b05..c86cc562f10 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -195,7 +195,7 @@ class AnnotatedHit class RNPxlSearch : public TOPPBase { - // fast or all-shifts scoring mode + // fast or all fragment adduct scoring mode bool fast_scoring_ = true; // nucleotides can form cross-link @@ -468,7 +468,7 @@ class RNPxlSearch : Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); - const int exp_z = exp_charges[index]; + const Size exp_z = exp_charges[index]; // found peak match if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) @@ -488,7 +488,7 @@ class RNPxlSearch : { for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { - for (int i = 0; i < partial_loss_template_z1_y_ions.size(); ++i) + for (Size i = 0; i < partial_loss_template_z1_y_ions.size(); ++i) { const double theo_mz = (partial_loss_template_z1_y_ions[i] + fa.mass + (z-1) * Constants::PROTON_MASS_U) / z; @@ -498,7 +498,7 @@ class RNPxlSearch : Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); - const int exp_z = exp_charges[index]; + const Size exp_z = exp_charges[index]; // found peak match if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) @@ -570,7 +570,7 @@ class RNPxlSearch : const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); - const int exp_z = exp_charges[index]; + const Size exp_z = exp_charges[index]; // found peak match if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) @@ -2055,6 +2055,119 @@ static void scoreShiftedFragments_( precursor_ion_sub_score_spectrum_generator.setParameters(param); } + // calculate PSMs using total loss scoring (no NA-shifted fragments) + static void addPSMsTotalLossScoring_( + const PeakSpectrum& exp_spectrum, + const StringView sequence, + const Size & mod_pep_idx, + const Size & rna_mod_idx, + const double & current_peptide_mass, + const double & exp_pc_mass, + const int & isotope_error, + const PeakSpectrum & total_loss_spectrum_z1, + const PeakSpectrum & total_loss_spectrum_z2, + const PeakSpectrum & a_ion_sub_score_spectrum, + const PeakSpectrum & precursor_sub_score_spectrum, + const PeakSpectrum & immonium_sub_score_spectrum, + const boost::math::normal & gaussian_mass_error, + const double & mass_error_prior_negatives, + const double & fragment_mass_tolerance, + const bool & fragment_mass_tolerance_unit_ppm, + vector & annotated_hits, + omp_lock_t & annotated_hits_lock, + const Size& report_top_hits + ) + { + const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); + + const PeakSpectrum & total_loss_spectrum = (exp_pc_charge < 3) ? total_loss_spectrum_z1 : total_loss_spectrum_z2; + + float total_loss_score(0), + immonium_sub_score(0), + precursor_sub_score(0), + a_ion_sub_score(0), + tlss_MIC(0), + tlss_err(1.0), + tlss_Morph(0), + tlss_modds(0); + + scoreTotalLossFragments_(exp_spectrum, + total_loss_spectrum, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + a_ion_sub_score_spectrum, + precursor_sub_score_spectrum, + immonium_sub_score_spectrum, + total_loss_score, + tlss_MIC, + tlss_err, + tlss_Morph, + tlss_modds, + immonium_sub_score, + precursor_sub_score, + a_ion_sub_score); + + const double total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; + + // super bad score + if (total_loss_score < MIN_HYPERSCORE + || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 + || tlss_modds < 1e-10 + || total_MIC < 0.01) + { + return; + } + + const double mass_error_ppm = (current_peptide_mass - exp_pc_mass) / exp_pc_mass * 1e6; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; + + // add peptide hit + AnnotatedHit ah; + ah.mass_error_p = mass_error_score; + + ah.sequence = sequence; // copy StringView + ah.peptide_mod_index = mod_pep_idx; + ah.total_loss_score = total_loss_score; + ah.MIC = tlss_MIC; + ah.err = tlss_err; + ah.Morph = tlss_Morph; + ah.modds = tlss_modds; + ah.immonium_score = immonium_sub_score; + ah.precursor_score = precursor_sub_score; + ah.a_ion_score = a_ion_sub_score; + + ah.total_MIC = total_MIC; + + ah.rna_mod_index = rna_mod_idx; + ah.isotope_error = isotope_error; + + // simple combined score in fast scoring: + ah.score = total_loss_score + ah.total_MIC + mass_error_score / 3.0; + + #ifdef DEBUG_RNPXLSEARCH + LOG_DEBUG << "best score in pre-score: " << score << endl; + #endif + + #ifdef _OPENMP + omp_set_lock(&(annotated_hits_lock)); + #endif + { + annotated_hits.emplace_back(move(ah)); + + // prevent vector from growing indefinitly (memory) but don't shrink the vector every time + if (annotated_hits.size() >= 2 * report_top_hits) + { + std::partial_sort(annotated_hits.begin(), annotated_hits.begin() + report_top_hits, annotated_hits.end(), AnnotatedHit::hasBetterScore); + annotated_hits.resize(report_top_hits); + } + } + #ifdef _OPENMP + omp_unset_lock(&(annotated_hits_lock)); + #endif + } + + + ExitCodes main_(int, const char**) override { // force initialization of residue db @@ -2742,95 +2855,32 @@ static void scoreShiftedFragments_( { for (auto l = low_it; l != up_it; ++l) { - //const double exp_pc_mass = l->first; - const Size &scan_index = l->second.first; - const int &isotope_error = l->second.second; - const PeakSpectrum &exp_spectrum = spectra[scan_index]; - float total_loss_score(0), - immonium_sub_score(0), - precursor_sub_score(0), - a_ion_sub_score(0), - tlss_MIC(0), - tlss_err(1.0), - tlss_Morph(0), - tlss_modds(0); - - const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); - PeakSpectrum & total_loss_spectrum = (exp_pc_charge < 3) ? total_loss_spectrum_z1 : total_loss_spectrum_z2; - - scoreTotalLossFragments_(exp_spectrum, - total_loss_spectrum, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - a_ion_sub_score_spectrum, - precursor_sub_score_spectrum, - immonium_sub_score_spectrum, - total_loss_score, - tlss_MIC, - tlss_err, - tlss_Morph, - tlss_modds, - immonium_sub_score, - precursor_sub_score, - a_ion_sub_score); - - const double total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; - - // super bad score - if (total_loss_score < MIN_HYPERSCORE - || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_modds < 1e-10 - || total_MIC < 0.01) - { - continue; - } - - const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; - const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; - - // add peptide hit - AnnotatedHit ah; - ah.mass_error_p = mass_error_score; - - ah.sequence = *cit; // copy StringView - ah.peptide_mod_index = mod_pep_idx; - ah.total_loss_score = total_loss_score; - ah.MIC = tlss_MIC; - ah.err = tlss_err; - ah.Morph = tlss_Morph; - ah.modds = tlss_modds; - ah.immonium_score = immonium_sub_score; - ah.precursor_score = precursor_sub_score; - ah.a_ion_score = a_ion_sub_score; - - ah.total_MIC = total_MIC; - - ah.rna_mod_index = rna_mod_index; - ah.isotope_error = isotope_error; - - // simple combined score in fast scoring: - ah.score = total_loss_score + ah.total_MIC + mass_error_score / 3.0; - -#ifdef DEBUG_RNPXLSEARCH - LOG_DEBUG << "best score in pre-score: " << score << endl; -#endif - -#ifdef _OPENMP - omp_set_lock(&(annotated_hits_lock[scan_index])); -#endif - { - annotated_hits[scan_index].emplace_back(move(ah)); - - // prevent vector from growing indefinitly (memory) but don't shrink the vector every time - if (annotated_hits[scan_index].size() >= 2 * report_top_hits) - { - std::partial_sort(annotated_hits[scan_index].begin(), annotated_hits[scan_index].begin() + report_top_hits, annotated_hits[scan_index].end(), AnnotatedHit::hasBetterScore); - annotated_hits[scan_index].resize(report_top_hits); - } - } -#ifdef _OPENMP - omp_unset_lock(&(annotated_hits_lock[scan_index])); -#endif + const Size & scan_index = l->second.first; + const int & isotope_error = l->second.second; + const double exp_pc_mass = l->first; + + // generate PSMs for spectrum[scan_index] and add them to annotated_hits[scan_index] + addPSMsTotalLossScoring_( + spectra[scan_index], + *cit, // string view on unmodified sequence + mod_pep_idx, // index of peptide mod + rna_mod_index, // index of RNA mod + current_peptide_mass, + exp_pc_mass, + isotope_error, + total_loss_spectrum_z1, + total_loss_spectrum_z2, + a_ion_sub_score_spectrum, + precursor_sub_score_spectrum, + immonium_sub_score_spectrum, + gaussian_mass_error, + mass_error_prior_negatives, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + annotated_hits[scan_index], + annotated_hits_lock[scan_index], + report_top_hits + ); } } } From 932c57e4d2deb1b96113474342c73b5d50e35b05 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 29 Mar 2019 13:06:39 +0100 Subject: [PATCH 028/471] [NOP] rearrange continue --- src/utils/RNPxlSearch.cpp | 28 +++++++++------------------- 1 file changed, 9 insertions(+), 19 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index c86cc562f10..8f44d578a15 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -2170,9 +2170,6 @@ static void scoreShiftedFragments_( ExitCodes main_(int, const char**) override { - // force initialization of residue db - static auto s = AASequence::fromString("GPAVLIMCFYWHKRQNEDST"); - ProgressLogger progresslogger; progresslogger.setLogType(log_type_); String in_mzml = getStringOption_("in"); @@ -2450,26 +2447,20 @@ static void scoreShiftedFragments_( #pragma omp atomic #endif ++count_peptides; - vector all_modified_peptides; const String unmodified_sequence = cit->getString(); + // only process peptides without ambiguous amino acids (placeholder / any amino acid) + if (unmodified_sequence.find_first_of("XBZ") != std::string::npos) continue; + // determine which residues might give rise to an immonium ion ImmoniumIonsInPeptide iip(unmodified_sequence); -#ifdef _OPENMP -#pragma omp critical (residuedb_access) -#endif - { - // only process peptides without ambiguous amino acids (placeholder / any amino acid) - if (unmodified_sequence.find_first_of("XBZ") == std::string::npos) - { - AASequence aas = AASequence::fromString(unmodified_sequence); - ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications.begin(), fixed_modifications.end(), aas); - ModifiedPeptideGenerator::applyVariableModifications(variable_modifications.begin(), variable_modifications.end(), aas, max_variable_mods_per_peptide, all_modified_peptides); - } - } - + AASequence aas = AASequence::fromString(unmodified_sequence); + ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications.begin(), fixed_modifications.end(), aas); + vector all_modified_peptides; + ModifiedPeptideGenerator::applyVariableModifications(variable_modifications.begin(), variable_modifications.end(), aas, max_variable_mods_per_peptide, all_modified_peptides); + for (SignedSize mod_pep_idx = 0; mod_pep_idx < (SignedSize)all_modified_peptides.size(); ++mod_pep_idx) { const AASequence& fixed_and_variable_modified_peptide = all_modified_peptides[mod_pep_idx]; @@ -2487,14 +2478,12 @@ static void scoreShiftedFragments_( // iterate over all NA sequences, calculate peptide mass and generate complete loss spectrum only once as this can potentially be reused Size rna_mod_index = 0; - // TODO: track the XL-able nt here for (std::map::const_iterator rna_mod_it = mm.mod_masses.begin(); rna_mod_it != mm.mod_masses.end(); ++rna_mod_it, ++rna_mod_index) { const double precursor_rna_mass = rna_mod_it->second; const double current_peptide_mass = current_peptide_mass_without_NA + precursor_rna_mass; // add NA mass - // TODO: const char xl_nucleotide; // can be none // determine MS2 precursors that match to the current peptide mass MassToScanMultiMap::const_iterator low_it, up_it; @@ -2527,6 +2516,7 @@ static void scoreShiftedFragments_( immonium_sub_score_spectrum.getStringDataArrays()[0]); immonium_sub_score_spectrum.sortByPosition(); precursor_ion_sub_score_spectrum_generator.getSpectrum(precursor_sub_score_spectrum, fixed_and_variable_modified_peptide, 1, 1); + // only generate first 4 a-ions as others are rarely observed a_ion_sub_score_spectrum_generator.getSpectrum(a_ion_sub_score_spectrum, fixed_and_variable_modified_peptide, 1, 1); a_ion_sub_score_spectrum.resize(4); From 2b5d983ff22a3240d25e7646b828e54f4fdd45f5 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Mon, 1 Apr 2019 10:39:32 +0200 Subject: [PATCH 029/471] [FIX] separate critical section may lead to scoring same protein sequence twice --- src/utils/RNPxlSearch.cpp | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 8f44d578a15..c1cc2c91d41 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -2432,17 +2432,14 @@ static void scoreShiftedFragments_( { already_processed = true; } + else + { + processed_petides.insert(*cit); + } } if (already_processed) { continue; } -#ifdef _OPENMP -#pragma omp critical (processed_peptides_access) -#endif - { - processed_petides.insert(*cit); - } - #ifdef _OPENMP #pragma omp atomic #endif From 17c06d6092559e48851556228153479c3b6d59db Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Mon, 1 Apr 2019 10:39:32 +0200 Subject: [PATCH 030/471] [FIX] separate critical section may lead to scoring same protein sequence twice --- src/utils/RNPxlSearch.cpp | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 8f44d578a15..90148304fb0 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -1872,7 +1872,7 @@ static void scoreShiftedFragments_( #pragma omp critical (peptide_ids_access) #endif { - peptide_ids.push_back(pi); + peptide_ids.push_back(std::move(pi)); } } } @@ -2432,17 +2432,14 @@ static void scoreShiftedFragments_( { already_processed = true; } + else + { + processed_petides.insert(*cit); + } } if (already_processed) { continue; } -#ifdef _OPENMP -#pragma omp critical (processed_peptides_access) -#endif - { - processed_petides.insert(*cit); - } - #ifdef _OPENMP #pragma omp atomic #endif From e93bdbfd7af3a8b6d1c13f19b00c93c2f804b12b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 1 Apr 2019 13:15:21 +0200 Subject: [PATCH 031/471] [NOP] move peptide in peptide generator --- src/openms/source/ANALYSIS/RNPXL/ModifiedPeptideGenerator.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/ModifiedPeptideGenerator.cpp b/src/openms/source/ANALYSIS/RNPXL/ModifiedPeptideGenerator.cpp index 20aac5160f1..0c6e9acaa2b 100644 --- a/src/openms/source/ANALYSIS/RNPXL/ModifiedPeptideGenerator.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/ModifiedPeptideGenerator.cpp @@ -339,7 +339,7 @@ namespace OpenMS { AASequence new_peptide = peptide; new_peptide.setModification(residue_index, variable_it->getFullName()); - all_modified_peptides.push_back(new_peptide); + all_modified_peptides.push_back(std::move(new_peptide)); } } } From 596382d467fcd7f1d1a04786039258537e2fa78a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 23 Apr 2019 15:57:36 +0200 Subject: [PATCH 032/471] nop --- src/utils/RNPxlSearch.cpp | 136 ++++++++++++++++++++++++++++++++++++-- 1 file changed, 129 insertions(+), 7 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 90148304fb0..285ffb8412b 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -417,6 +417,127 @@ class RNPxlSearch : return z; } + static void scorePeptideLadderIons_( + const vector& total_loss_template_z1_b_ions, + const vector& total_loss_template_z1_y_ions, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const DataArrays::IntegerDataArray& exp_charges, + std::vector& intensity_sum) + { + OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); + OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); + OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); + OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_y_ions.size(), "Sum array needs to be of same size as y-ion array"); + OPENMS_PRECONDITION(total_loss_template_z1_b_ions.size() == total_loss_template_z1_y_ions.size(), "b- and y-ion arrays must have same size."); + OPENMS_PRECONDITION(total_loss_template_z1_b_ions.size() > 0, "b- and y-ion arrays must not be empty."); + + double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); + const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 + std::vector b_ions(N, 0.0), y_ions(N, 0.0); + + // maximum charge considered + const Size max_z = std::min(pc_charge - 1, 2U); + + // match b-ions only + for (Size z = 1; z <= max_z; ++z) + { + for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) + { + for (Size i = 0; i < total_loss_template_z1_b_ions.size(); ++i) + { + const double theo_mz = (total_loss_template_z1_b_ions[i] + (z-1) * Constants::PROTON_MASS_U) / z; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + + // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak + Size index = exp_spectrum.findNearest(theo_mz); + + const double exp_mz = exp_spectrum[index].getMZ(); + const Size exp_z = exp_charges[index]; + + // found peak match + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + const double intensity = exp_spectrum[index].getIntensity(); + b_mean_err += intensity * std::abs(theo_mz - exp_mz); + dot_product += intensity ; + b_ions[i] += intensity ; + } + } + } + } + + // match y-ions + for (Size z = 1; z <= max_z; ++z) + { + for (Size i = 0; i < total_loss_template_z1_y_ions.size(); ++i) + { + const double theo_mz = (total_loss_template_z1_y_ions[i] + (z-1) * Constants::PROTON_MASS_U) / z; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + + // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak + Size index = exp_spectrum.findNearest(theo_mz); + + const double exp_mz = exp_spectrum[index].getMZ(); + const Size exp_z = exp_charges[index]; + + // found peak match + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + const double intensity = exp_spectrum[index].getIntensity(); + y_mean_err += intensity * std::abs(theo_mz - exp_mz); + dot_product += intensity; + y_ions[N-1 - i] += intensity; + } + } + } + + UInt y_ion_count(0), b_ion_count(0); + double b_sum(0.0); + for (Size i = 0; i != b_ions.size(); ++i) + { + if (b_ions[i] > 0) + { + intensity_sum[i] += b_ions[i]; + b_sum += b_ions[i]; + ++b_ion_count; + } + } + + double y_sum(0.0); + for (Size i = 0; i != y_ions.size(); ++i) + { + if (y_ions[i] > 0) + { + intensity_sum[i] += y_ions[i]; + y_sum += y_ions[i]; + ++y_ion_count; + } + } + + // TODO: calculate this once and store in exp_spectrum meta data? + double TIC = std::accumulate(exp_spectrum.begin(), exp_spectrum.end(), 0.0, + [&](double a, const Peak1D& b) { return a + b.getIntensity(); }); + + if (y_ion_count == 0 && b_ion_count == 0) + { + plss_hyperScore = 0; + plss_MIC = 0; + plss_Morph = 0; + plss_err = fragment_mass_tolerance_unit_ppm ? 2000.0 * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + } + else + { + const double yFact = logfactorial_(y_ion_count); + const double bFact = logfactorial_(b_ion_count); + plss_hyperScore = log1p(dot_product) + yFact + bFact; + plss_MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); + plss_MIC /= TIC; + plss_Morph = b_ion_count + y_ion_count + plss_MIC; + plss_err = (y_mean_err + b_mean_err)/(b_sum + y_sum); + } + } static void scoreShiftedLadderIons_( const vector& partial_loss_modification, @@ -544,7 +665,7 @@ class RNPxlSearch : plss_hyperScore = 0; plss_MIC = 0; plss_Morph = 0; - plss_err = fragment_mass_tolerance_unit_ppm ? 2000.0 * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance;; + plss_err = fragment_mass_tolerance_unit_ppm ? 2000.0 * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; } else { @@ -555,7 +676,7 @@ class RNPxlSearch : plss_MIC /= TIC; plss_Morph = b_ion_count + y_ion_count + plss_MIC; plss_err = (y_mean_err + b_mean_err)/(b_sum + y_sum); - } + } // match (partially) shifted precusor ions z = 1..pc_charge for (double pc_loss : {0.0, -18.010565, -17.026548} ) // normal, loss of water, loss of ammonia @@ -2105,7 +2226,7 @@ static void scoreShiftedFragments_( tlss_modds, immonium_sub_score, precursor_sub_score, - a_ion_sub_score); + a_ion_sub_score) const double total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; @@ -2999,7 +3120,7 @@ static void scoreShiftedFragments_( return EXECUTION_OK; } - +/* // determine main score and sub scores of peaks without shifts static void scoreTotalLossFragments_(const PeakSpectrum &exp_spectrum, const PeakSpectrum &total_loss_spectrum, @@ -3017,12 +3138,13 @@ static void scoreShiftedFragments_( float &precursor_sub_score, float &a_ion_sub_score) { - total_loss_score = HyperScore::compute(fragment_mass_tolerance, + total_loss_score = RNPxlSearch::computeHyperScore(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, exp_spectrum.getIntegerDataArrays()[0], total_loss_spectrum, - total_loss_spectrum.getIntegerDataArrays()[0]); + total_loss_spectrum.getIntegerDataArrays()[0], + aa_coverage); // bad score, likely wihout any single matching peak if (total_loss_score < MIN_HYPERSCORE) @@ -3081,7 +3203,7 @@ static void scoreShiftedFragments_( a_ion_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } } - +*/ static void scorePartialLossFragments_(const Size peptide_size, const PeakSpectrum &exp_spectrum, double fragment_mass_tolerance, From e842eca6fa32337c5e61582a71a27d4efbff070d Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 24 Apr 2019 17:58:17 +0200 Subject: [PATCH 033/471] probably broke everything by changing total loss scoring to new fast mode --- src/utils/RNPxlSearch.cpp | 364 ++++++++++++++++++++++++++++---------- 1 file changed, 274 insertions(+), 90 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 285ffb8412b..326a21324b4 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -177,7 +177,6 @@ class AnnotatedHit float partial_loss_score = 0; float immonium_score = 0; float precursor_score = 0; - float a_ion_score = 0; float marker_ions_score = 0; float best_localization_score = 0; @@ -417,14 +416,24 @@ class RNPxlSearch : return z; } - static void scorePeptideLadderIons_( - const vector& total_loss_template_z1_b_ions, - const vector& total_loss_template_z1_y_ions, - double fragment_mass_tolerance, - bool fragment_mass_tolerance_unit_ppm, + static void scorePeptideIons_( const PeakSpectrum& exp_spectrum, const DataArrays::IntegerDataArray& exp_charges, - std::vector& intensity_sum) + const vector& total_loss_template_z1_b_ions, + const vector& total_loss_template_z1_y_ions, + const double peptide_mass_without_NA, + const unsigned int pc_charge, + const ImmoniumIonsInPeptide& iip, + const double fragment_mass_tolerance, + const bool fragment_mass_tolerance_unit_ppm, + std::vector& intensity_sum, + float& hyperScore, + float& MIC, + float& Morph, + float& modds, + float& err, + float& pc_MIC, + float& im_MIC) { OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); @@ -438,16 +447,17 @@ class RNPxlSearch : std::vector b_ions(N, 0.0), y_ions(N, 0.0); // maximum charge considered - const Size max_z = std::min(pc_charge - 1, 2U); + const unsigned int max_z = std::max(3U, static_cast(std::min(pc_charge - 1, 2U))); - // match b-ions only - for (Size z = 1; z <= max_z; ++z) - { - for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) + // match b- and a-ions (we record a-ions as b-ions) + for (double diff2b : {0.0, -27.994915} ) // b-ion and a-ion ('CO' mass diff from b- to a-ion) + { + for (Size z = 1; z <= max_z; ++z) { for (Size i = 0; i < total_loss_template_z1_b_ions.size(); ++i) { - const double theo_mz = (total_loss_template_z1_b_ions[i] + (z-1) * Constants::PROTON_MASS_U) / z; + const double theo_mz = (total_loss_template_z1_b_ions[i] + diff2b + + (z-1) * Constants::PROTON_MASS_U) / z; const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak @@ -465,7 +475,7 @@ class RNPxlSearch : b_ions[i] += intensity ; } } - } + } } // match y-ions @@ -522,21 +532,119 @@ class RNPxlSearch : if (y_ion_count == 0 && b_ion_count == 0) { - plss_hyperScore = 0; - plss_MIC = 0; - plss_Morph = 0; - plss_err = fragment_mass_tolerance_unit_ppm ? 2000.0 * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + hyperScore = 0; + MIC = 0; + Morph = 0; + err = fragment_mass_tolerance_unit_ppm ? 2000.0 * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; } else { const double yFact = logfactorial_(y_ion_count); const double bFact = logfactorial_(b_ion_count); - plss_hyperScore = log1p(dot_product) + yFact + bFact; - plss_MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); - plss_MIC /= TIC; - plss_Morph = b_ion_count + y_ion_count + plss_MIC; - plss_err = (y_mean_err + b_mean_err)/(b_sum + y_sum); + hyperScore = log1p(dot_product) + yFact + bFact; + MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); + MIC /= TIC; + Morph = b_ion_count + y_ion_count + MIC; + err = (y_mean_err + b_mean_err)/(b_sum + y_sum); + } + + // match precusor ions z = 1..pc_charge + for (double pc_loss : {0.0, -18.010565, -17.026548} ) // normal, loss of water, loss of ammonia + { + const double peptide_mass = peptide_mass_without_NA + pc_loss; + for (Size z = 1; z <= pc_charge; ++z) + { + const double theo_mz = (peptide_mass + z * Constants::PROTON_MASS_U) / z; + + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + Size index = exp_spectrum.findNearest(theo_mz); + const double exp_mz = exp_spectrum[index].getMZ(); + const Size exp_z = exp_charges[index]; + + // found peak match + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + const double intensity = exp_spectrum[index].getIntensity(); + pc_MIC += intensity; + } + } } + pc_MIC /= TIC; + + // shifted immonium ions + + // lambda to match one peak and sum up in score + auto match_one_peak_z1 = [&](const double& theo_mz, float& score) + { + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + auto index = exp_spectrum.findNearest(theo_mz); + if (exp_charges[index] == 1 && + std::abs(theo_mz - exp_spectrum[index].getMZ()) < max_dist_dalton) // found peak match + { + score += exp_spectrum[index].getIntensity(); + } + }; + + // TODO: complete with others from DOI: 10.1021/pr3007045 + // A Systematic Investigation into the Nature of Tryptic HCD Spectra + + static const double imY = EmpiricalFormula("C8H10NO").getMonoWeight(); // 85% + static const double imW = EmpiricalFormula("C10H11N2").getMonoWeight(); // 84% + static const double imF = EmpiricalFormula("C8H10N").getMonoWeight(); // 84% + static const double imL = EmpiricalFormula("C5H12N").getMonoWeight(); // I/L 76% + static const double imH = EmpiricalFormula("C5H8N3").getMonoWeight(); // 70% + static const double imC = EmpiricalFormula("C2H6NS").getMonoWeight(); // CaC 61% +// static const double imQ = EmpiricalFormula("?").getMonoWeight(); // 52% +// static const double imE = EmpiricalFormula("?").getMonoWeight(); // 37% +// static const double imN = EmpiricalFormula("?").getMonoWeight(); // 11% +// static const double imD = EmpiricalFormula("?").getMonoWeight(); // 4% +// static const double imM = EmpiricalFormula("?").getMonoWeight(); // 3% + static const double imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); // 2% + + static const double imP = EmpiricalFormula("C4H8N").getMonoWeight(); //? + + if (iip.Y) + { + match_one_peak_z1(imY, im_MIC); + } + if (iip.W) + { + match_one_peak_z1(imW, im_MIC); + } + if (iip.F) + { + match_one_peak_z1(imF, im_MIC); + } + if (iip.H) + { + match_one_peak_z1(imH, im_MIC); + } + if (iip.C) + { + match_one_peak_z1(imC, im_MIC); + } + if (iip.P) + { + match_one_peak_z1(imP, im_MIC); + } + if (iip.L) + { + match_one_peak_z1(imL, im_MIC); + } + if (iip.K) + { + match_one_peak_z1(imK1, im_MIC); + } + if (iip.M) + { + match_one_peak_z1(104.05285, im_MIC); + } + im_MIC /= TIC; + + // if we only have 1 peak assume some kind of average error to not underestimate the real error to much + err = Morph > 2 ? err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; + modds = matchOddsScore_(total_loss_template_z1_b_ions.size() + + total_loss_template_z1_y_ions.size(), (int)Morph); } static void scoreShiftedLadderIons_( @@ -546,8 +654,8 @@ class RNPxlSearch : const double peptide_mass_without_NA, const unsigned int pc_charge, const ImmoniumIonsInPeptide& iip, - double fragment_mass_tolerance, - bool fragment_mass_tolerance_unit_ppm, + const double fragment_mass_tolerance, + const bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const DataArrays::IntegerDataArray& exp_charges, std::vector& intensity_sum, @@ -555,6 +663,7 @@ class RNPxlSearch : float& plss_MIC, float& plss_Morph, float& plss_err, + float& plss_modds, float& plss_pc_MIC, float& plss_im_MIC) { @@ -570,7 +679,7 @@ class RNPxlSearch : std::vector b_ions(N, 0.0), y_ions(N, 0.0); // maximum charge considered - const Size max_z = std::min(pc_charge - 1, 2U); + const unsigned int max_z = std::max(3U, static_cast(std::min(pc_charge - 1, 2U))); // match b- and a-ions (we record a-ions as b-ions) for (double diff2b : {0.0, -27.994915} ) // b-ion and a-ion ('CO' mass diff from b- to a-ion) @@ -773,6 +882,11 @@ class RNPxlSearch : } } plss_im_MIC /= TIC; + + // if we only have 1 peak assume some kind of average error to not underestimate the real error to much + plss_err = plss_Morph > 2 ? plss_err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; + plss_modds = matchOddsScore_(partial_loss_template_z1_b_ions.size() + + partial_loss_template_z1_y_ions.size(), (int)plss_Morph); } static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) @@ -917,13 +1031,9 @@ static void scoreShiftedFragments_( plss_MIC, plss_Morph, plss_err, + plss_modds, plss_pc_MIC, plss_im_MIC); - - // if we only have 1 peak assume some kind of average error to not underestimate the real error to much - plss_err = plss_Morph > 2 ? plss_err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - plss_modds = matchOddsScore_(partial_loss_template_z1_b_ions.size() - + partial_loss_template_z1_y_ions.size(), (int)plss_Morph); } #ifdef DEBUG_RNPXLSEARCH LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; @@ -1943,7 +2053,6 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("RNPxl:total_loss_score"), ah.total_loss_score); ph.setMetaValue(String("RNPxl:immonium_score"), ah.immonium_score); ph.setMetaValue(String("RNPxl:precursor_score"), ah.precursor_score); - ph.setMetaValue(String("RNPxl:a_ion_score"), ah.a_ion_score); ph.setMetaValue(String("RNPxl:marker_ions_score"), ah.marker_ions_score); ph.setMetaValue(String("RNPxl:partial_loss_score"), ah.partial_loss_score); @@ -2028,7 +2137,6 @@ static void scoreShiftedFragments_( << "RNPxl:modds" << "RNPxl:immonium_score" << "RNPxl:precursor_score" - << "RNPxl:a_ion_score" << "RNPxl:marker_ions_score" << "RNPxl:partial_loss_score" << "RNPxl:MIC" @@ -2183,52 +2291,55 @@ static void scoreShiftedFragments_( const Size & mod_pep_idx, const Size & rna_mod_idx, const double & current_peptide_mass, + const double & current_peptide_mass_without_NA, const double & exp_pc_mass, + const ImmoniumIonsInPeptide & iip, const int & isotope_error, - const PeakSpectrum & total_loss_spectrum_z1, - const PeakSpectrum & total_loss_spectrum_z2, - const PeakSpectrum & a_ion_sub_score_spectrum, - const PeakSpectrum & precursor_sub_score_spectrum, - const PeakSpectrum & immonium_sub_score_spectrum, + const vector & total_loss_template_z1_b_ions, + const vector & total_loss_template_z1_y_ions, const boost::math::normal & gaussian_mass_error, const double & mass_error_prior_negatives, const double & fragment_mass_tolerance, const bool & fragment_mass_tolerance_unit_ppm, vector & annotated_hits, omp_lock_t & annotated_hits_lock, - const Size& report_top_hits - ) + const Size& report_top_hits) { const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); - const PeakSpectrum & total_loss_spectrum = (exp_pc_charge < 3) ? total_loss_spectrum_z1 : total_loss_spectrum_z2; - float total_loss_score(0), immonium_sub_score(0), precursor_sub_score(0), - a_ion_sub_score(0), tlss_MIC(0), tlss_err(1.0), tlss_Morph(0), - tlss_modds(0); - - scoreTotalLossFragments_(exp_spectrum, - total_loss_spectrum, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - a_ion_sub_score_spectrum, - precursor_sub_score_spectrum, - immonium_sub_score_spectrum, - total_loss_score, - tlss_MIC, - tlss_err, - tlss_Morph, - tlss_modds, - immonium_sub_score, - precursor_sub_score, - a_ion_sub_score) - - const double total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; + tlss_modds(0), + pc_MIC(0), + im_MIC(0); + + vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + + scorePeptideIons_( + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + total_loss_template_z1_b_ions, + total_loss_template_z1_y_ions, + current_peptide_mass_without_NA, + exp_pc_charge, + iip, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + intensity_sum, + total_loss_score, + tlss_MIC, + tlss_Morph, + tlss_modds, + tlss_err, + pc_MIC, + im_MIC + ); + + const double total_MIC = tlss_MIC + im_MIC + pc_MIC; // super bad score if (total_loss_score < MIN_HYPERSCORE @@ -2255,7 +2366,6 @@ static void scoreShiftedFragments_( ah.modds = tlss_modds; ah.immonium_score = immonium_sub_score; ah.precursor_score = precursor_sub_score; - ah.a_ion_score = a_ion_sub_score; ah.total_MIC = total_MIC; @@ -2287,7 +2397,30 @@ static void scoreShiftedFragments_( #endif } + // check for misannotation (absolute m/z instead of offset) and correct + void checkAndCorrectIsolationWindows_(MSExperiment& e) + { + bool isolation_windows_reannotated = false; + for (MSSpectrum & s : e) + { + if (s.getMSLevel() == 2 && s.getPrecursors().size() == 1) + { + Precursor& p = s.getPrecursors()[0]; + if (p.getIsolationWindowLowerOffset() > 100.0 && p.getIsolationWindowUpperOffset() > 100.0) + { + isolation_windows_reannotated = true; + p.setIsolationWindowLowerOffset(p.getIsolationWindowLowerOffset() - p.getMZ()); + p.setIsolationWindowUpperOffset(p.getIsolationWindowUpperOffset() - p.getMZ()); + } + } + } + + if (isolation_windows_reannotated) + { + LOG_WARN << "Isolation windows format was incorrect. Reannotated." << endl; + } + } ExitCodes main_(int, const char**) override { @@ -2421,6 +2554,8 @@ static void scoreShiftedFragments_( int nMS1 = std::count_if(tmp_spectra.begin(), tmp_spectra.end(), [](MSSpectrum& s){return s.getMSLevel() == 1;}); if (nMS1 != 0) { + // if isolation windows are properly annotated and correct if necessary + checkAndCorrectIsolationWindows_(tmp_spectra); purities = PrecursorPurity::computePrecursorPurities(tmp_spectra, precursor_mass_tolerance, precursor_mass_tolerance_unit_ppm); } } // free spectra @@ -2466,6 +2601,7 @@ static void scoreShiftedFragments_( a_ion_sub_score_spectrum_generator, immonium_ion_sub_score_spectrum_generator, precursor_ion_sub_score_spectrum_generator); + // preallocate storage for PSMs vector > annotated_hits(spectra.size(), vector()); @@ -2585,7 +2721,7 @@ static void scoreShiftedFragments_( double current_peptide_mass_without_NA = fixed_and_variable_modified_peptide.getMonoWeight(); //create empty theoretical spectrum. total_loss_spectrum_z2 contains both charge 1 and charge 2 peaks - PeakSpectrum total_loss_spectrum_z1, total_loss_spectrum_z2; + vector total_loss_template_z1_b_ions, total_loss_template_z1_y_ions; // spectrum containing additional peaks for sub scoring PeakSpectrum immonium_sub_score_spectrum, @@ -2622,10 +2758,11 @@ static void scoreShiftedFragments_( // add peaks for b- and y- ions with charge 1 (sorted by m/z) // total / complete loss spectra are generated for fast and (slow) full scoring - if (total_loss_spectrum_z1.empty()) // only create complete loss spectrum once as this is rather costly and need only to be done once per petide + if (total_loss_template_z1_b_ions.empty()) // only create complete loss spectrum once as this is rather costly and need only to be done once per petide { - total_loss_spectrum_generator.getSpectrum(total_loss_spectrum_z1, fixed_and_variable_modified_peptide, 1, 1); - total_loss_spectrum_generator.getSpectrum(total_loss_spectrum_z2, fixed_and_variable_modified_peptide, 1, 2); + generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::ResidueType::BIon, total_loss_template_z1_b_ions); + generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::ResidueType::YIon, total_loss_template_z1_y_ions); +/* immonium_ion_sub_score_spectrum_generator.getSpectrum(immonium_sub_score_spectrum, fixed_and_variable_modified_peptide, 1, 1); RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( unmodified_sequence, @@ -2640,6 +2777,7 @@ static void scoreShiftedFragments_( a_ion_sub_score_spectrum.resize(4); a_ion_sub_score_spectrum.getStringDataArrays()[0].resize(4); a_ion_sub_score_spectrum.getIntegerDataArrays()[0].resize(4); +*/ } if (!fast_scoring_) @@ -2652,24 +2790,47 @@ static void scoreShiftedFragments_( if (precursor_rna_adduct == "none") { // score peptide without NA (same method as fast scoring) - for (auto l = low_it; l != up_it; ++l) + for (auto & l = low_it; l != up_it; ++l) { //const double exp_pc_mass = l->first; const Size & scan_index = l->second.first; const int & isotope_error = l->second.second; const PeakSpectrum & exp_spectrum = spectra[scan_index]; const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); - PeakSpectrum & total_loss_spectrum = (exp_pc_charge < 3) ? total_loss_spectrum_z1 : total_loss_spectrum_z2; - float total_loss_score(0), + float hyperScore(0), immonium_sub_score(0), precursor_sub_score(0), a_ion_sub_score(0), tlss_MIC(0), tlss_err(0), tlss_Morph(0), - tlss_modds(0); - + tlss_modds(0), + pc_MIC, + im_MIC; + + vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + scorePeptideIons_( + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + total_loss_template_z1_b_ions, + total_loss_template_z1_y_ions, + current_peptide_mass_without_NA, + exp_pc_charge, + iip, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + intensity_sum, + hyperScore, + tlss_MIC, + tlss_Morph, + tlss_modds, + tlss_err, + pc_MIC, + im_MIC + ); + + /* scoreTotalLossFragments_(exp_spectrum, total_loss_spectrum, fragment_mass_tolerance, @@ -2685,9 +2846,10 @@ static void scoreShiftedFragments_( immonium_sub_score, precursor_sub_score, a_ion_sub_score); + */ // bad score or less then two peaks matching - if (total_loss_score < MIN_HYPERSCORE + if (hyperScore < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 || tlss_modds < 1e-10 || tlss_MIC < 0.01) @@ -2708,10 +2870,9 @@ static void scoreShiftedFragments_( ah.err = tlss_err; ah.Morph = tlss_Morph; ah.modds = tlss_modds; - ah.total_loss_score = total_loss_score; + ah.total_loss_score = hyperScore; ah.immonium_score = immonium_sub_score; ah.precursor_score = precursor_sub_score; - ah.a_ion_score = a_ion_sub_score; ah.total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; ah.rna_mod_index = rna_mod_index; @@ -2818,11 +2979,11 @@ static void scoreShiftedFragments_( generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::YIon, partial_loss_template_z1_yions); } - for (auto l = low_it; l != up_it; ++l) + for (auto & l = low_it; l != up_it; ++l) { - const Size& scan_index = l->second.first; - const int& isotope_error = l->second.second; - const PeakSpectrum& exp_spectrum = spectra[scan_index]; + const Size & scan_index = l->second.first; + const int & isotope_error = l->second.second; + const PeakSpectrum & exp_spectrum = spectra[scan_index]; float tlss_MIC(0), tlss_err(1.0), tlss_Morph(0), @@ -2832,11 +2993,33 @@ static void scoreShiftedFragments_( a_ion_sub_score(0), partial_loss_sub_score(0), marker_ions_sub_score(0), - tlss_score(0); + hyperScore(0), + pc_MIC, + im_MIC; const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); - PeakSpectrum & total_loss_spectrum = (exp_pc_charge < 3) ? total_loss_spectrum_z1 : total_loss_spectrum_z2; + vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + scorePeptideIons_( + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + total_loss_template_z1_b_ions, + total_loss_template_z1_y_ions, + current_peptide_mass_without_NA, + exp_pc_charge, + iip, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + intensity_sum, + hyperScore, + tlss_MIC, + tlss_Morph, + tlss_modds, + tlss_err, + pc_MIC, + im_MIC + ); + /* scoreTotalLossFragments_(exp_spectrum, total_loss_spectrum, fragment_mass_tolerance, @@ -2861,6 +3044,7 @@ static void scoreShiftedFragments_( { continue; } + */ float plss_MIC(0), plss_err(1.0), @@ -2909,7 +3093,7 @@ static void scoreShiftedFragments_( ah.sequence = *cit; // copy StringView ah.peptide_mod_index = mod_pep_idx; - ah.total_loss_score = tlss_score; + ah.total_loss_score = hyperScore; ah.MIC = tlss_MIC; ah.err = tlss_err; ah.Morph = tlss_Morph; @@ -2922,7 +3106,6 @@ static void scoreShiftedFragments_( ah.pl_im_MIC = plss_im_MIC; ah.immonium_score = immonium_sub_score; ah.precursor_score = precursor_sub_score; - ah.a_ion_score = a_ion_sub_score; ah.cross_linked_nucleotide = cross_linked_nucleotide; ah.total_MIC = total_MIC; // scores from shifted peaks @@ -2961,11 +3144,11 @@ static void scoreShiftedFragments_( } else // fast scoring { - for (auto l = low_it; l != up_it; ++l) + for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; const int & isotope_error = l->second.second; - const double exp_pc_mass = l->first; + const double & exp_pc_mass = l->first; // generate PSMs for spectrum[scan_index] and add them to annotated_hits[scan_index] addPSMsTotalLossScoring_( @@ -2974,13 +3157,12 @@ static void scoreShiftedFragments_( mod_pep_idx, // index of peptide mod rna_mod_index, // index of RNA mod current_peptide_mass, + current_peptide_mass_without_NA, exp_pc_mass, + iip, isotope_error, - total_loss_spectrum_z1, - total_loss_spectrum_z2, - a_ion_sub_score_spectrum, - precursor_sub_score_spectrum, - immonium_sub_score_spectrum, + total_loss_template_z1_b_ions, + total_loss_template_z1_y_ions, gaussian_mass_error, mass_error_prior_negatives, fragment_mass_tolerance, @@ -3204,6 +3386,8 @@ static void scoreShiftedFragments_( } } */ + + static void scorePartialLossFragments_(const Size peptide_size, const PeakSpectrum &exp_spectrum, double fragment_mass_tolerance, From 7b6cd477ec106d45eb00678c0f0a6c5310e62d59 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 25 Apr 2019 13:51:54 +0200 Subject: [PATCH 034/471] before cleanup --- src/openms/source/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.cpp index 5e5a1f49c64..bc371787c77 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.cpp @@ -56,7 +56,6 @@ RNPxlMarkerIonExtractor::MarkerIonsType RNPxlMarkerIonExtractor::extractMarkerIo PeakSpectrum spec(s); Normalizer normalizer; normalizer.filterSpectrum(spec); - spec.sortByPosition(); // for each nucleotide with marker ions for (MarkerIonsType::iterator it = marker_ions.begin(); it != marker_ions.end(); ++it) From e05b916250401ad055df9b55a910d29d3f076121 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 25 Apr 2019 15:10:56 +0200 Subject: [PATCH 035/471] clean-up --- src/utils/RNPxlSearch.cpp | 406 +++++--------------------------------- 1 file changed, 51 insertions(+), 355 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 326a21324b4..bf3f61bab35 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -32,6 +32,9 @@ // $Authors: Timo Sachsenberg $ // -------------------------------------------------------------------------- + // TODO: + // - precursor correction + #include #include #include @@ -194,12 +197,8 @@ class AnnotatedHit class RNPxlSearch : public TOPPBase { - // fast or all fragment adduct scoring mode - bool fast_scoring_ = true; - - // nucleotides can form cross-link - set can_xl_; - + bool fast_scoring_ = true; // fast or all fragment adduct scoring mode + set can_xl_; ///< nucleotides that can form cross-links public: RNPxlSearch() : @@ -503,6 +502,7 @@ class RNPxlSearch : } } + // determine b+a and y-ion count UInt y_ion_count(0), b_ion_count(0); double b_sum(0.0); for (Size i = 0; i != b_ions.size(); ++i) @@ -526,9 +526,11 @@ class RNPxlSearch : } } - // TODO: calculate this once and store in exp_spectrum meta data? - double TIC = std::accumulate(exp_spectrum.begin(), exp_spectrum.end(), 0.0, - [&](double a, const Peak1D& b) { return a + b.getIntensity(); }); + OPENMS_PRECONDITION(exp_spectrum.getFloatDataArrays().size() == 1, "Exactly one float data array expected."); + OPENMS_PRECONDITION(exp_spectrum.getFloatDataArrays()[0].getName() == "TIC", "No TIC stored in spectrum meta data."); + OPENMS_PRECONDITION(exp_spectrum.getFloatDataArrays()[0].size() == 1, "Exactly one TIC expected."); + + const double& TIC = exp_spectrum.getFloatDataArrays()[0][0]; if (y_ion_count == 0 && b_ion_count == 0) { @@ -765,9 +767,7 @@ class RNPxlSearch : } } - // TODO: calculate this once and store in exp_spectrum meta data? - double TIC = std::accumulate(exp_spectrum.begin(), exp_spectrum.end(), 0.0, - [&](double a, const Peak1D& b) { return a + b.getIntensity(); }); + const double& TIC = exp_spectrum.getFloatDataArrays()[0][0]; if (y_ion_count == 0 && b_ion_count == 0) { @@ -813,7 +813,8 @@ class RNPxlSearch : } plss_pc_MIC /= TIC; - // shifted immonium ions + //////////////////////////////////////////////////////////////////////////////// + // match shifted immonium ions // lambda to match one peak and sum up in score auto match_one_peak_z1 = [&](const double& theo_mz, float& score) @@ -891,29 +892,6 @@ class RNPxlSearch : static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) { -/* - coeff. std. err. Z-score P>|z| -not isXL: -1 RNPxl:total_loss_score 0.21721652155697285 0.09483942249623674 2.2903610739046 0.022000394091310493 -1 RNPxl:mass_error_p 1.9988345415208777 0.5320970905622918 3.756522215538927 1.7229098345827865E-4 -1 RNPxl:modds 0.5842539236790404 0.14707508807450823 3.972487328262264 7.112602099945686E-5 -1 RNPxl:total_MIC 4.059968526608637 0.6997810753887223 5.801769538213591 6.561872156751747E-9 -1 Constant -6.486416409280039 1.0530367515627284 -6.159724624666768 7.287158654278869E-10 - - isXL: - coeff. std. err. Z-score P>|z| -RNPxl:pl_MIC 2.3319284783288805 1.443968593532589 1.614944042947601 0.10632281328213189 -RNPxl:pl_Morph -0.1821314450150078 0.0992607992067629 -1.8348778820088194 0.06652378554713212 -RNPxl:mass_error_p 1.2107674392113372 0.6479149468312813 1.8687135481790702 0.06166267808238679 -RNPxl:total_loss_score 0.25318342707227187 0.11026025896332549 2.2962346492990293 0.02166246839013919 -RNPxl:modds 0.5446999629799386 0.21771187712636128 2.501930396125295 0.012351820599275531 -RNPxl:partial_loss_score 0.12472562244230834 0.04757766801488459 2.6215160945527667 0.008753962882873556 -RNPxl:Morph 0.4688059636415974 0.14790453990151833 3.169652290279595 0.0015262145546381944 -RNPxl:MIC 4.0386886051238 1.161533977368853 3.477030103133424 5.070008902814394E-4 -Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.5283262211340798E-7 - -*/ - if (!isXL) { return - 6.486416409280039 @@ -933,38 +911,6 @@ Constant -6.648631037190969 1.2666197103005374 -5.249113828817186 1.528326221134 + 1.2107674392113372 * ah.mass_error_p + 2.3319284783288805 * ah.pl_MIC; } -// return ah.total_loss_score + ah.total_MIC + ah.mass_error_p / 3.0; -/* - return - 4.2 - + 1.995 * ah.total_MIC - + 1.115 * ah.mass_error_p - + 0.504 * ah.total_loss_score - - 0.021 * ah.Morph - - 0.011 * ah.modds - + 0.084 * ah.partial_loss_score - - 0.244 * ah.pl_Morph - - 1.077 * static_cast(isXL); -*/ -/* - return + 0.995 - + 7.142 * ( 0.058 * ah.total_loss_score - 0.900) - + 0.802 * ( 33.35 * ah.immonium_score - 1.148) - + 0.327 * ( 73.64 * ah.precursor_score - 0.821) - + 0.748 * ( 22.014 * ah.marker_ions_score - 0.903) - + 0.746 * ( 0.043 * ah.partial_loss_score - 0.472) - - 1.788 * ( 301.0 * ah.err - 1.771) - - 1.292 * (240.825 * ah.pl_err - 1.323) - + 2.324 * static_cast(isXL); -*/ - /* old version - return - 2.493 - + 7.239 * (0.058 * ah.total_loss_score - 0.900) - + 1.381 * (26.965 * ah.marker_ions_score - 0.300) - + 1.178 * (0.043 * ah.partial_loss_score - 0.472) - - 1.934 * (300.828 * ah.err - 1.774) - - 0.358 * (240.441 * ah.pl_err - 1.316); - */ } /* @@ -1144,6 +1090,14 @@ static void scoreShiftedFragments_( for (Size i = 0; i != spec.size(); ++i) cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << "\t" << ia[i] << endl; #endif + + // calculate TIC and store in float data array + double TIC = std::accumulate(spec.begin(), spec.end(), 0.0, + [&](double a, const Peak1D& b) { return a + b.getIntensity(); }); + spec.getFloatDataArrays().clear(); + spec.getFloatDataArrays().resize(1); + spec.getFloatDataArrays()[0].push_back(TIC); + spec.getFloatDataArrays()[0].setName("TIC"); } } @@ -1161,10 +1115,24 @@ static void scoreShiftedFragments_( const vector& fixed_modifications, const vector& variable_modifications, Size max_variable_mods_per_peptide, - const TheoreticalSpectrumGenerator& partial_loss_spectrum_generator, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const RNPxlParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts) { + TheoreticalSpectrumGenerator partial_loss_spectrum_generator; + auto param = partial_loss_spectrum_generator.getParameters(); + param.setValue("add_first_prefix_ion", "true"); + param.setValue("add_abundant_immonium_ions", "false"); // we add them manually for charge 1 + param.setValue("add_precursor_peaks", "true"); + param.setValue("add_all_precursor_charges", "false"); // we add them manually for every charge + param.setValue("add_metainfo", "true"); + param.setValue("add_a_ions", "true"); + param.setValue("add_b_ions", "true"); + param.setValue("add_c_ions", "false"); + param.setValue("add_x_ions", "false"); + param.setValue("add_y_ions", "true"); + param.setValue("add_z_ions", "false"); + partial_loss_spectrum_generator.setParameters(param); + assert(exp.size() == annotated_hits.size()); #ifdef DEBUG_RNPXLSEARCH @@ -1325,7 +1293,7 @@ static void scoreShiftedFragments_( plss_Morph(0), plss_modds(0); - scorePartialLossFragments_( unmodified_sequence.size(), + postScorePartialLossFragments_( unmodified_sequence.size(), exp_spectrum, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, @@ -2216,74 +2184,6 @@ static void scoreShiftedFragments_( } } - void initializeSpectrumGenerators(TheoreticalSpectrumGenerator &total_loss_spectrum_generator, - TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, - TheoreticalSpectrumGenerator &a_ion_sub_score_spectrum_generator, - TheoreticalSpectrumGenerator &immonium_ion_sub_score_spectrum_generator, - TheoreticalSpectrumGenerator &precursor_ion_sub_score_spectrum_generator) const - { - Param param(total_loss_spectrum_generator.getParameters()); - param.setValue("add_first_prefix_ion", "true"); - param.setValue("add_abundant_immonium_ions", "false"); - param.setValue("add_precursor_peaks", "false"); - param.setValue("add_metainfo", "true"); - param.setValue("add_a_ions", "false"); - param.setValue("add_b_ions", "true"); - param.setValue("add_c_ions", "false"); - param.setValue("add_x_ions", "false"); - param.setValue("add_y_ions", "true"); - param.setValue("add_z_ions", "false"); - total_loss_spectrum_generator.setParameters(param); - - param = partial_loss_spectrum_generator.getParameters(); - param.setValue("add_first_prefix_ion", "true"); - param.setValue("add_abundant_immonium_ions", "false"); // we add them manually for charge 1 - param.setValue("add_precursor_peaks", "true"); - param.setValue("add_all_precursor_charges", "false"); // we add them manually for every charge - param.setValue("add_metainfo", "true"); - param.setValue("add_a_ions", "true"); - param.setValue("add_b_ions", "true"); - param.setValue("add_c_ions", "false"); - param.setValue("add_x_ions", "false"); - param.setValue("add_y_ions", "true"); - param.setValue("add_z_ions", "false"); - partial_loss_spectrum_generator.setParameters(param); - - // generator for sub scores for a-ions, immonium and precursor peaksparam = a_ion_sub_score_spectrum_generator.getParameters(); - param.setValue("add_abundant_immonium_ions", "false"); - param.setValue("add_precursor_peaks", "false"); - param.setValue("add_a_ions", "true"); - param.setValue("add_b_ions", "false"); - param.setValue("add_c_ions", "false"); - param.setValue("add_x_ions", "false"); - param.setValue("add_y_ions", "false"); - param.setValue("add_z_ions", "false"); - param.setValue("add_metainfo", "true"); - a_ion_sub_score_spectrum_generator.setParameters(param); - param = immonium_ion_sub_score_spectrum_generator.getParameters(); - param.setValue("add_abundant_immonium_ions", "true"); - param.setValue("add_precursor_peaks", "false"); - param.setValue("add_a_ions", "false"); - param.setValue("add_b_ions", "false"); - param.setValue("add_c_ions", "false"); - param.setValue("add_x_ions", "false"); - param.setValue("add_y_ions", "false"); - param.setValue("add_z_ions", "false"); - param.setValue("add_metainfo", "true"); - immonium_ion_sub_score_spectrum_generator.setParameters(param); - param = precursor_ion_sub_score_spectrum_generator.getParameters(); - param.setValue("add_abundant_immonium_ions", "false"); - param.setValue("add_precursor_peaks", "true"); - param.setValue("add_a_ions", "false"); - param.setValue("add_b_ions", "false"); - param.setValue("add_c_ions", "false"); - param.setValue("add_x_ions", "false"); - param.setValue("add_y_ions", "false"); - param.setValue("add_z_ions", "false"); - param.setValue("add_metainfo", "true"); - precursor_ion_sub_score_spectrum_generator.setParameters(param); - } - // calculate PSMs using total loss scoring (no NA-shifted fragments) static void addPSMsTotalLossScoring_( const PeakSpectrum& exp_spectrum, @@ -2308,8 +2208,6 @@ static void scoreShiftedFragments_( const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); float total_loss_score(0), - immonium_sub_score(0), - precursor_sub_score(0), tlss_MIC(0), tlss_err(1.0), tlss_Morph(0), @@ -2364,8 +2262,8 @@ static void scoreShiftedFragments_( ah.err = tlss_err; ah.Morph = tlss_Morph; ah.modds = tlss_modds; - ah.immonium_score = immonium_sub_score; - ah.precursor_score = precursor_sub_score; + ah.immonium_score = im_MIC; + ah.precursor_score = pc_MIC; ah.total_MIC = total_MIC; @@ -2560,8 +2458,6 @@ static void scoreShiftedFragments_( } } // free spectra - //TODO: precursor correction - PeakFileOptions options; options.clearMSLevels(); options.addMSLevel(2); @@ -2590,18 +2486,7 @@ static void scoreShiftedFragments_( spectra, multimap_mass_2_scan_index); - // initialize spectrum generators (generated ions, etc.) - TheoreticalSpectrumGenerator total_loss_spectrum_generator; - TheoreticalSpectrumGenerator partial_loss_spectrum_generator; - TheoreticalSpectrumGenerator a_ion_sub_score_spectrum_generator; - TheoreticalSpectrumGenerator immonium_ion_sub_score_spectrum_generator; - TheoreticalSpectrumGenerator precursor_ion_sub_score_spectrum_generator; - initializeSpectrumGenerators(total_loss_spectrum_generator, - partial_loss_spectrum_generator, - a_ion_sub_score_spectrum_generator, - immonium_ion_sub_score_spectrum_generator, - precursor_ion_sub_score_spectrum_generator); - + // preallocate storage for PSMs vector > annotated_hits(spectra.size(), vector()); @@ -2707,7 +2592,7 @@ static void scoreShiftedFragments_( // only process peptides without ambiguous amino acids (placeholder / any amino acid) if (unmodified_sequence.find_first_of("XBZ") != std::string::npos) continue; - // determine which residues might give rise to an immonium ion + // determine which residues might give rise to an immonium ion ImmoniumIonsInPeptide iip(unmodified_sequence); AASequence aas = AASequence::fromString(unmodified_sequence); @@ -2724,10 +2609,7 @@ static void scoreShiftedFragments_( vector total_loss_template_z1_b_ions, total_loss_template_z1_y_ions; // spectrum containing additional peaks for sub scoring - PeakSpectrum immonium_sub_score_spectrum, - a_ion_sub_score_spectrum, - precursor_sub_score_spectrum, - marker_ions_sub_score_spectrum; + PeakSpectrum marker_ions_sub_score_spectrum; // iterate over all NA sequences, calculate peptide mass and generate complete loss spectrum only once as this can potentially be reused Size rna_mod_index = 0; @@ -2756,28 +2638,11 @@ static void scoreShiftedFragments_( if (low_it == up_it) { continue; } // no matching precursor in data // add peaks for b- and y- ions with charge 1 (sorted by m/z) - // total / complete loss spectra are generated for fast and (slow) full scoring if (total_loss_template_z1_b_ions.empty()) // only create complete loss spectrum once as this is rather costly and need only to be done once per petide { generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::ResidueType::BIon, total_loss_template_z1_b_ions); generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::ResidueType::YIon, total_loss_template_z1_y_ions); -/* - immonium_ion_sub_score_spectrum_generator.getSpectrum(immonium_sub_score_spectrum, fixed_and_variable_modified_peptide, 1, 1); - RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( - unmodified_sequence, - immonium_sub_score_spectrum, - immonium_sub_score_spectrum.getIntegerDataArrays()[0], - immonium_sub_score_spectrum.getStringDataArrays()[0]); - immonium_sub_score_spectrum.sortByPosition(); - precursor_ion_sub_score_spectrum_generator.getSpectrum(precursor_sub_score_spectrum, fixed_and_variable_modified_peptide, 1, 1); - - // only generate first 4 a-ions as others are rarely observed - a_ion_sub_score_spectrum_generator.getSpectrum(a_ion_sub_score_spectrum, fixed_and_variable_modified_peptide, 1, 1); - a_ion_sub_score_spectrum.resize(4); - a_ion_sub_score_spectrum.getStringDataArrays()[0].resize(4); - a_ion_sub_score_spectrum.getIntegerDataArrays()[0].resize(4); -*/ } if (!fast_scoring_) @@ -2830,24 +2695,6 @@ static void scoreShiftedFragments_( im_MIC ); - /* - scoreTotalLossFragments_(exp_spectrum, - total_loss_spectrum, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - a_ion_sub_score_spectrum, - precursor_sub_score_spectrum, - immonium_sub_score_spectrum, - total_loss_score, - tlss_MIC, - tlss_err, - tlss_Morph, - tlss_modds, - immonium_sub_score, - precursor_sub_score, - a_ion_sub_score); - */ - // bad score or less then two peaks matching if (hyperScore < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 @@ -2930,37 +2777,6 @@ static void scoreShiftedFragments_( PeakSpectrum marker_ions_sub_score_spectrum_z1; - /*, - partial_loss_spectrum_z1, - partial_loss_spectrum_z2; - - // nucleotide is associated with certain NA-related fragment losses? - if (!partial_loss_modification.empty()) - { - // shifted b- / y- / a-ions - RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - current_peptide_mass_without_NA, - precursor_rna_adduct, - precursor_rna_mass, - 1, - partial_loss_modification, - partial_loss_template_z1, - partial_loss_template_z2, - partial_loss_template_z3, - partial_loss_spectrum_z1); - - RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - current_peptide_mass_without_NA, - precursor_rna_adduct, - precursor_rna_mass, - 2, // don't know the charge of the precursor at that point - partial_loss_modification, - partial_loss_template_z1, - partial_loss_template_z2, - partial_loss_template_z3, - partial_loss_spectrum_z2); - } -*/ // add shifted marker ions marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation @@ -3019,32 +2835,15 @@ static void scoreShiftedFragments_( pc_MIC, im_MIC ); - /* - scoreTotalLossFragments_(exp_spectrum, - total_loss_spectrum, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - a_ion_sub_score_spectrum, - precursor_sub_score_spectrum, - immonium_sub_score_spectrum, - tlss_score, - tlss_MIC, - tlss_err, - tlss_Morph, - tlss_modds, - immonium_sub_score, - precursor_sub_score, - a_ion_sub_score); // bad score or less then two peaks matching - if (tlss_score < MIN_HYPERSCORE + if (hyperScore < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 || tlss_MIC < 0.01 || tlss_modds < 1e-10) { continue; } - */ float plss_MIC(0), plss_err(1.0), @@ -3075,8 +2874,9 @@ static void scoreShiftedFragments_( const double total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score + plss_MIC + plss_pc_MIC + plss_im_MIC; - // less then two shifted peaks? seems to throw out some good hits ??? -/* if ( partial_loss_sub_score < MIN_HYPERSCORE // at least one peak with 10% of max intensity +/* + // less then two shifted peaks? seems to throw out some good hits ??? + if ( partial_loss_sub_score < MIN_HYPERSCORE // at least one peak with 10% of max intensity || plss_Morph < MIN_SHIFTED_IONS + 1.0 // > 1 shifted peaks || total_MIC < 0.01 // less than 1% explained peaks ) @@ -3187,6 +2987,7 @@ static void scoreShiftedFragments_( vector protein_ids; progresslogger.startProgress(0, 1, "Post-processing PSMs..."); + /////////////////////////////////////////////////////////////////////////////////////////////////// // Localization // @@ -3204,19 +3005,6 @@ static void scoreShiftedFragments_( progresslogger.startProgress(0, 1, "localization..."); - // create spectrum generator. For convenience we add more peak types here. - Param param(total_loss_spectrum_generator.getParameters()); - param.setValue("add_first_prefix_ion", "true"); - param.setValue("add_abundant_immonium_ions", "true"); - param.setValue("add_precursor_peaks", "true"); - param.setValue("add_metainfo", "true"); - param.setValue("add_a_ions", "false"); - param.setValue("add_b_ions", "true"); - param.setValue("add_c_ions", "false"); - param.setValue("add_x_ions", "false"); - param.setValue("add_y_ions", "true"); - param.setValue("add_z_ions", "false"); - total_loss_spectrum_generator.setParameters(param); postScoreHits_(spectra, annotated_hits, @@ -3225,7 +3013,6 @@ static void scoreShiftedFragments_( fixed_modifications, variable_modifications, max_variable_mods_per_peptide, - partial_loss_spectrum_generator, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_fragment_adducts); @@ -3302,93 +3089,8 @@ static void scoreShiftedFragments_( return EXECUTION_OK; } -/* - // determine main score and sub scores of peaks without shifts - static void scoreTotalLossFragments_(const PeakSpectrum &exp_spectrum, - const PeakSpectrum &total_loss_spectrum, - double fragment_mass_tolerance, - bool fragment_mass_tolerance_unit_ppm, - const PeakSpectrum &a_ion_sub_score_spectrum, - const PeakSpectrum &precursor_sub_score_spectrum, - const PeakSpectrum &immonium_sub_score_spectrum, - float &total_loss_score, - float &tlss_MIC, - float &tlss_err, - float &tlss_Morph, - float &tlss_modds, - float &immonium_sub_score, - float &precursor_sub_score, - float &a_ion_sub_score) - { - total_loss_score = RNPxlSearch::computeHyperScore(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - total_loss_spectrum, - total_loss_spectrum.getIntegerDataArrays()[0], - aa_coverage); - - // bad score, likely wihout any single matching peak - if (total_loss_score < MIN_HYPERSCORE) - { - // cap total loss error to a large value - float ft_da = fragment_mass_tolerance_unit_ppm ? 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0 : 2.0 * fragment_mass_tolerance; - if (tlss_err > ft_da) tlss_err = ft_da; - return; - } - - immonium_sub_score = 0; - precursor_sub_score = 0; - a_ion_sub_score = 0; - auto const & tl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - total_loss_spectrum, - total_loss_spectrum.getIntegerDataArrays()[0]); - - tlss_MIC = tl_sub_scores.TIC != 0 ? tl_sub_scores.MIC / tl_sub_scores.TIC : 0; - tlss_Morph = tl_sub_scores.score; - - // if we only have 1 or peaks assume some kind of average error to not underestimate the real error to much - tlss_err = tlss_Morph > 2 ? tl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - tlss_modds = matchOddsScore_(total_loss_spectrum.size(), (int)tlss_Morph); // (int)Morph == number of matched peaks - - if (!immonium_sub_score_spectrum.empty()) - { - auto const & r = MorpheusScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - immonium_sub_score_spectrum, - immonium_sub_score_spectrum.getIntegerDataArrays()[0]); - immonium_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; - } - if (!precursor_sub_score_spectrum.empty()) - { - auto const & r = MorpheusScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - precursor_sub_score_spectrum, - precursor_sub_score_spectrum.getIntegerDataArrays()[0]); - precursor_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; - } - if (!a_ion_sub_score_spectrum.empty()) - { - auto const & r = MorpheusScore::compute(fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - a_ion_sub_score_spectrum, - a_ion_sub_score_spectrum.getIntegerDataArrays()[0]); - a_ion_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; - } - } -*/ - - static void scorePartialLossFragments_(const Size peptide_size, + static void postScorePartialLossFragments_(const Size peptide_size, const PeakSpectrum &exp_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, @@ -3414,14 +3116,7 @@ static void scoreShiftedFragments_( marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0]); marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } - //TODO: these are currently empty -/* - if (!shifted_immonium_ions_sub_score_spectrum.empty()) - { - shifted_immonium_ions_sub_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, shifted_immonium_ions_sub_score_spectrum); - shifted_immonium_ions_sub_score(0), - } -*/ + if (!partial_loss_spectrum_z1.empty()) // check if we generated partial loss spectra { vector intensity_sum(peptide_size, 0.0); @@ -3446,6 +3141,7 @@ static void scoreShiftedFragments_( pl_spec->getIntegerDataArrays()[0]); plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; plss_Morph = pl_sub_scores.score; + // if we only have 1 peak assume some kind of average error to not underestimate the real error to much plss_err = plss_Morph > 2 ? pl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; plss_modds = matchOddsScore_(pl_spec->size(), (int)plss_Morph); From 28bccc51cf8c51a643edcc6ecf874159403beb87 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 25 Apr 2019 16:04:37 +0200 Subject: [PATCH 036/471] [FIX] lower/upper window --- src/utils/RNPxlSearch.cpp | 33 +++++++++++++++++++++++++++------ 1 file changed, 27 insertions(+), 6 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index bf3f61bab35..b8c4e574c36 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -2298,7 +2298,8 @@ static void scoreShiftedFragments_( // check for misannotation (absolute m/z instead of offset) and correct void checkAndCorrectIsolationWindows_(MSExperiment& e) { - bool isolation_windows_reannotated = false; + int isolation_windows_reannotated(0); + int isolation_windows_reannotation_error(0); for (MSSpectrum & s : e) { @@ -2307,16 +2308,36 @@ static void scoreShiftedFragments_( Precursor& p = s.getPrecursors()[0]; if (p.getIsolationWindowLowerOffset() > 100.0 && p.getIsolationWindowUpperOffset() > 100.0) { - isolation_windows_reannotated = true; - p.setIsolationWindowLowerOffset(p.getIsolationWindowLowerOffset() - p.getMZ()); - p.setIsolationWindowUpperOffset(p.getIsolationWindowUpperOffset() - p.getMZ()); + // in most cases lower and upper offset contain the absolute values. + // if that is the case we use those + double left = -(p.getIsolationWindowLowerOffset() - p.getMZ()); + double right = p.getIsolationWindowUpperOffset() - p.getMZ(); + if (left > 0.0 && right > 0.0) + { + p.setIsolationWindowLowerOffset(left); + p.setIsolationWindowUpperOffset(right); + } + else // in some files from PD the target m/z is sometimes to the left of the lower isolation window (bug?) + { + // something wrong with left boundary... use information from right + left = p.getMZ() - right; + p.setIsolationWindowLowerOffset(left); + p.setIsolationWindowUpperOffset(right); + isolation_windows_reannotation_error++; + } + isolation_windows_reannotated++; } } } - if (isolation_windows_reannotated) + if (isolation_windows_reannotated > 0) { - LOG_WARN << "Isolation windows format was incorrect. Reannotated." << endl; + LOG_WARN << "Isolation windows format was incorrect. Reannotated " << isolation_windows_reannotated << " precursors windows. " << endl; + if (isolation_windows_reannotation_error > 0) + { + LOG_WARN << "Reannotation failed for " << isolation_windows_reannotation_error + << " precursors windows because the target m/z was outside of boundaries." << endl; + } } } From 90021ea5c19a73d7a06d159e6ec4d6a2b9cc96eb Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 26 Apr 2019 10:41:26 +0200 Subject: [PATCH 037/471] [FEATURE] ladder and sequence score --- src/utils/RNPxlSearch.cpp | 156 +++++++++++++++++++++++++------------- 1 file changed, 105 insertions(+), 51 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index b8c4e574c36..35e5b30acc5 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -182,6 +182,9 @@ class AnnotatedHit float precursor_score = 0; float marker_ions_score = 0; + float ladder_score = 0; + float sequence_score = 0; + float best_localization_score = 0; String localization_scores; String best_localization; @@ -436,13 +439,13 @@ class RNPxlSearch : { OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); - OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); - OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_y_ions.size(), "Sum array needs to be of same size as y-ion array"); OPENMS_PRECONDITION(total_loss_template_z1_b_ions.size() == total_loss_template_z1_y_ions.size(), "b- and y-ion arrays must have same size."); OPENMS_PRECONDITION(total_loss_template_z1_b_ions.size() > 0, "b- and y-ion arrays must not be empty."); + OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); + OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_y_ions.size(), "Sum array needs to be of same size as y-ion array"); double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); - const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 + const Size N = intensity_sum.size(); std::vector b_ions(N, 0.0), y_ions(N, 0.0); // maximum charge considered @@ -553,11 +556,9 @@ class RNPxlSearch : // match precusor ions z = 1..pc_charge for (double pc_loss : {0.0, -18.010565, -17.026548} ) // normal, loss of water, loss of ammonia { - const double peptide_mass = peptide_mass_without_NA + pc_loss; for (Size z = 1; z <= pc_charge; ++z) { - const double theo_mz = (peptide_mass + z * Constants::PROTON_MASS_U) / z; - + const double theo_mz = (peptide_mass_without_NA + pc_loss + z * Constants::PROTON_MASS_U) / z; const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); @@ -918,7 +919,6 @@ class RNPxlSearch : */ static void scoreShiftedFragments_( const vector &partial_loss_modification, - const Size peptide_size, const ImmoniumIonsInPeptide& iip, const PeakSpectrum &exp_spectrum, const double peptide_mass_without_NA, @@ -927,6 +927,7 @@ static void scoreShiftedFragments_( const vector &partial_loss_template_z1_b_ions, const vector &partial_loss_template_z1_y_ions, const PeakSpectrum &marker_ions_sub_score_spectrum_z1, + vector& intensity_sum, float &partial_loss_sub_score, float &marker_ions_sub_score, float &plss_MIC, @@ -936,6 +937,10 @@ static void scoreShiftedFragments_( float &plss_pc_MIC, float &plss_im_MIC) { + OPENMS_PRECONDITION(!partial_loss_template_z1_b_ions.empty(), "Empty partial loss spectrum provided."); + OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); + OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_y_ions.size(), "Sum array needs to be of same size as y-ion array"); + const SignedSize& exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); //const double exp_pc_mz = exp_spectrum.getPrecursors()[0].getMZ(); @@ -957,30 +962,25 @@ static void scoreShiftedFragments_( shifted_immonium_ions_sub_score(0), } */ - if (!partial_loss_template_z1_b_ions.empty()) // check if we generated partial loss spectra - { - vector intensity_sum(peptide_size - 1, 0.0); - - scoreShiftedLadderIons_( - partial_loss_modification, - partial_loss_template_z1_b_ions, - partial_loss_template_z1_y_ions, - peptide_mass_without_NA, - exp_pc_charge, - iip, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], - intensity_sum, - partial_loss_sub_score, - plss_MIC, - plss_Morph, - plss_err, - plss_modds, - plss_pc_MIC, - plss_im_MIC); - } + scoreShiftedLadderIons_( + partial_loss_modification, + partial_loss_template_z1_b_ions, + partial_loss_template_z1_y_ions, + peptide_mass_without_NA, + exp_pc_charge, + iip, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[0], + intensity_sum, + partial_loss_sub_score, + plss_MIC, + plss_Morph, + plss_err, + plss_modds, + plss_pc_MIC, + plss_im_MIC); #ifdef DEBUG_RNPXLSEARCH LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif @@ -2056,6 +2056,8 @@ static void scoreShiftedFragments_( ph.setPeakAnnotations(ah.fragment_annotations); ph.setMetaValue("isotope_error", static_cast(ah.isotope_error)); + ph.setMetaValue(String("RNPxl:ladder_score"), ah.ladder_score); + ph.setMetaValue(String("RNPxl:sequence_score"), ah.sequence_score); ph.setMetaValue("rank", rank); // set the amino acid sequence (for complete loss spectra this is just the variable and modified peptide. For partial loss spectra it additionally contains the loss induced modification) ph.setSequence(fixed_and_variable_modified_peptide); @@ -2118,7 +2120,10 @@ static void scoreShiftedFragments_( << "RNPxl:pl_im_MIC" << "RNPxl:total_MIC" << "RNPxl:RNA_MASS_z0" + << "RNPxl:ladder_score" + << "RNPxl:sequence_score" << "precursor_intensity_log10"; + if (!purities.empty()) feature_set << "precursor_purity"; search_parameters.setMetaValue("feature_extractor", "TOPP_PSMFeatureExtractor"); @@ -2270,6 +2275,11 @@ static void scoreShiftedFragments_( ah.rna_mod_index = rna_mod_idx; ah.isotope_error = isotope_error; + auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); + ah.ladder_score = ladderScore_(range); + range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); + ah.sequence_score = ladderScore_(range); + // simple combined score in fast scoring: ah.score = total_loss_score + ah.total_MIC + mass_error_score / 3.0; @@ -2341,6 +2351,51 @@ static void scoreShiftedFragments_( } } + // returns iterator on start of longest non-zero sequence and end on one-after non-zero sequence (complete ladder) + template + static pair longestCompleteLadder_(Iterator b, Iterator e) + { + int max_l = 0; + Iterator best_start(b); + for(auto i = b; i != e;) // iterate once over vector + { + for (; i != e && *i <= 0.0; ++i) {}; // skip zeros + if (i == e) // end? + { + return make_pair(best_start, best_start + max_l); + } + unsigned int l = 0; + Iterator start(i); + for (; i != e && *i > 0.0; ++i) { ++l; } // count sequence of non-zeros + if (l > max_l) // longer sequence found? + { + best_start = start; + max_l = l; + } + if (i == e) // end? + { + return make_pair(best_start, best_start + max_l); + } + } + return make_pair(best_start, best_start + max_l); + } + + template + static float ladderScore_(pair p) + { + float MIC(0); + int count(0); + for (; p.first != p.second; ++p.first) + { + if (*p.first > 0.0) + { + MIC += *p.first; + ++count; + } + } + return count + MIC; // Morph score of matched (complete / partial) ladder + } + ExitCodes main_(int, const char**) override { ProgressLogger progresslogger; @@ -2685,15 +2740,12 @@ static void scoreShiftedFragments_( const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); float hyperScore(0), - immonium_sub_score(0), - precursor_sub_score(0), - a_ion_sub_score(0), tlss_MIC(0), tlss_err(0), tlss_Morph(0), tlss_modds(0), - pc_MIC, - im_MIC; + pc_MIC(0), + im_MIC(0); vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); scorePeptideIons_( @@ -2714,12 +2766,12 @@ static void scoreShiftedFragments_( tlss_err, pc_MIC, im_MIC - ); + ); // bad score or less then two peaks matching if (hyperScore < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_modds < 1e-10 + || tlss_modds < 1e-10 || tlss_MIC < 0.01) { continue; @@ -2739,13 +2791,16 @@ static void scoreShiftedFragments_( ah.Morph = tlss_Morph; ah.modds = tlss_modds; ah.total_loss_score = hyperScore; - ah.immonium_score = immonium_sub_score; - ah.precursor_score = precursor_sub_score; - ah.total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score; + ah.immonium_score = im_MIC; + ah.precursor_score = pc_MIC; + ah.total_MIC = tlss_MIC + im_MIC + pc_MIC; ah.rna_mod_index = rna_mod_index; ah.isotope_error = isotope_error; + ah.ladder_score = ladderScore_(make_pair(intensity_sum.begin(), intensity_sum.end())); + ah.sequence_score = ladderScore_(longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end())); + // combined score ah.score = RNPxlSearch::calculateCombinedScore(ah, false); @@ -2825,14 +2880,11 @@ static void scoreShiftedFragments_( tlss_err(1.0), tlss_Morph(0), tlss_modds(0), - immonium_sub_score(0), - precursor_sub_score(0), - a_ion_sub_score(0), partial_loss_sub_score(0), marker_ions_sub_score(0), hyperScore(0), - pc_MIC, - im_MIC; + pc_MIC(0), + im_MIC(0); const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); @@ -2874,7 +2926,6 @@ static void scoreShiftedFragments_( plss_im_MIC(0); scoreShiftedFragments_( partial_loss_modification, - unmodified_sequence.size(), iip, exp_spectrum, current_peptide_mass_without_NA, @@ -2883,6 +2934,7 @@ static void scoreShiftedFragments_( partial_loss_template_z1_bions, partial_loss_template_z1_yions, marker_ions_sub_score_spectrum_z1, + intensity_sum, partial_loss_sub_score, marker_ions_sub_score, plss_MIC, @@ -2892,8 +2944,7 @@ static void scoreShiftedFragments_( plss_pc_MIC, plss_im_MIC); - const double total_MIC = tlss_MIC + immonium_sub_score + a_ion_sub_score + precursor_sub_score + - plss_MIC + plss_pc_MIC + plss_im_MIC; + const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC; /* // less then two shifted peaks? seems to throw out some good hits ??? @@ -2916,6 +2967,8 @@ static void scoreShiftedFragments_( ah.peptide_mod_index = mod_pep_idx; ah.total_loss_score = hyperScore; ah.MIC = tlss_MIC; + ah.immonium_score = im_MIC; + ah.precursor_score = pc_MIC; ah.err = tlss_err; ah.Morph = tlss_Morph; ah.modds = tlss_modds; @@ -2925,8 +2978,6 @@ static void scoreShiftedFragments_( ah.pl_modds = plss_modds; ah.pl_pc_MIC = plss_pc_MIC; ah.pl_im_MIC = plss_im_MIC; - ah.immonium_score = immonium_sub_score; - ah.precursor_score = precursor_sub_score; ah.cross_linked_nucleotide = cross_linked_nucleotide; ah.total_MIC = total_MIC; // scores from shifted peaks @@ -2936,6 +2987,9 @@ static void scoreShiftedFragments_( ah.rna_mod_index = rna_mod_index; ah.isotope_error = isotope_error; + ah.ladder_score = ladderScore_(make_pair(intensity_sum.begin(), intensity_sum.end())); + ah.sequence_score = ladderScore_(longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end())); + // combined score ah.score = RNPxlSearch::calculateCombinedScore(ah, true); From 1d4c57725b133b6eef2ef145f8cfb5d2a4784716 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 26 Apr 2019 20:43:47 +0200 Subject: [PATCH 038/471] [FIX] sometimes also right isolation window offset seems to be off --- src/utils/RNPxlSearch.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 35e5b30acc5..87053006e7d 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -2327,10 +2327,11 @@ static void scoreShiftedFragments_( p.setIsolationWindowLowerOffset(left); p.setIsolationWindowUpperOffset(right); } - else // in some files from PD the target m/z is sometimes to the left of the lower isolation window (bug?) + else // in some files from PD the target m/z is sometimes outside the isolation window (bug?) { - // something wrong with left boundary... use information from right - left = p.getMZ() - right; + double half_w = (right - left) / 2.0; + left = p.getMZ() - half_w; + right = p.getMZ() + half_w; p.setIsolationWindowLowerOffset(left); p.setIsolationWindowUpperOffset(right); isolation_windows_reannotation_error++; From 9448784b8487375847ba454fe4bb64e03a67c183 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 7 May 2019 12:34:36 +0200 Subject: [PATCH 039/471] [FIX] percentage of covered bonds --- src/utils/RNPxlSearch.cpp | 42 +++++++++++++++++++++------------------ 1 file changed, 23 insertions(+), 19 deletions(-) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 87053006e7d..af181c33f27 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -449,7 +449,7 @@ class RNPxlSearch : std::vector b_ions(N, 0.0), y_ions(N, 0.0); // maximum charge considered - const unsigned int max_z = std::max(3U, static_cast(std::min(pc_charge - 1, 2U))); + const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); // match b- and a-ions (we record a-ions as b-ions) for (double diff2b : {0.0, -27.994915} ) // b-ion and a-ion ('CO' mass diff from b- to a-ion) @@ -682,7 +682,7 @@ class RNPxlSearch : std::vector b_ions(N, 0.0), y_ions(N, 0.0); // maximum charge considered - const unsigned int max_z = std::max(3U, static_cast(std::min(pc_charge - 1, 2U))); + const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); // match b- and a-ions (we record a-ions as b-ions) for (double diff2b : {0.0, -27.994915} ) // b-ion and a-ion ('CO' mass diff from b- to a-ion) @@ -954,14 +954,7 @@ static void scoreShiftedFragments_( marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0]); marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } - //TODO: these are currently empty -/* - if (!shifted_immonium_ions_sub_score_spectrum.empty()) - { - shifted_immonium_ions_sub_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, shifted_immonium_ions_sub_score_spectrum); - shifted_immonium_ions_sub_score(0), - } -*/ + scoreShiftedLadderIons_( partial_loss_modification, partial_loss_template_z1_b_ions, @@ -2276,9 +2269,12 @@ static void scoreShiftedFragments_( ah.isotope_error = isotope_error; auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); - ah.ladder_score = ladderScore_(range); + ah.ladder_score = ladderScore_(range) / (double)intensity_sum.size(); range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); - ah.sequence_score = ladderScore_(range); + if (range.second != range.first) + { + ah.sequence_score = ladderScore_(range) / (double)(range.second - range.first); + } // simple combined score in fast scoring: ah.score = total_loss_score + ah.total_MIC + mass_error_score / 3.0; @@ -2772,7 +2768,6 @@ static void scoreShiftedFragments_( // bad score or less then two peaks matching if (hyperScore < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_modds < 1e-10 || tlss_MIC < 0.01) { continue; @@ -2799,8 +2794,13 @@ static void scoreShiftedFragments_( ah.rna_mod_index = rna_mod_index; ah.isotope_error = isotope_error; - ah.ladder_score = ladderScore_(make_pair(intensity_sum.begin(), intensity_sum.end())); - ah.sequence_score = ladderScore_(longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end())); + auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); + ah.ladder_score = ladderScore_(range) / (double)intensity_sum.size(); + range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); + if (range.second != range.first) + { + ah.sequence_score = ladderScore_(range) / (double)(range.second - range.first); + } // combined score ah.score = RNPxlSearch::calculateCombinedScore(ah, false); @@ -2913,8 +2913,7 @@ static void scoreShiftedFragments_( // bad score or less then two peaks matching if (hyperScore < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_MIC < 0.01 - || tlss_modds < 1e-10) + || tlss_MIC < 0.01) { continue; } @@ -2988,8 +2987,13 @@ static void scoreShiftedFragments_( ah.rna_mod_index = rna_mod_index; ah.isotope_error = isotope_error; - ah.ladder_score = ladderScore_(make_pair(intensity_sum.begin(), intensity_sum.end())); - ah.sequence_score = ladderScore_(longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end())); + auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); + ah.ladder_score = ladderScore_(range) / (double)intensity_sum.size(); + range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); + if (range.second != range.first) + { + ah.sequence_score = ladderScore_(range) / (double)(range.second - range.first); + } // combined score ah.score = RNPxlSearch::calculateCombinedScore(ah, true); From 8c0a556e6184b9482c8e5c813940ef809cc53def Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 15 May 2019 17:13:33 +0200 Subject: [PATCH 040/471] [FEATURE] ladder score update, isXL isphospho --- src/topp/FileInfo.cpp | 1 + src/topp/IDFilter.cpp | 14 ++++++------- src/utils/RNPxlSearch.cpp | 42 ++++++++++++++++++++++++++++++++++----- 3 files changed, 45 insertions(+), 12 deletions(-) diff --git a/src/topp/FileInfo.cpp b/src/topp/FileInfo.cpp index b6a3a5baf19..df7f993d650 100644 --- a/src/topp/FileInfo.cpp +++ b/src/topp/FileInfo.cpp @@ -679,6 +679,7 @@ class TOPPFileInfo : public TOPPBase proteins.insert(temp_hits[j].getAccession()); } } + if (peptide_length.empty()) { // avoid invalid-range exception when computing mean() peptide_length.push_back(0); diff --git a/src/topp/IDFilter.cpp b/src/topp/IDFilter.cpp index f77ad6b0244..600a47a5c8f 100644 --- a/src/topp/IDFilter.cpp +++ b/src/topp/IDFilter.cpp @@ -619,13 +619,6 @@ class TOPPIDFilter : IDFilter::keepNBestHits(proteins, best_n_prot); } - if (getFlag_("remove_decoys")) - { - LOG_INFO << "Removing decoy hits..." << endl; - IDFilter::removeDecoyHits(peptides); - IDFilter::removeDecoyHits(proteins); - } - // remove peptide hits with meta values: if (remove_meta_enabled) @@ -676,6 +669,13 @@ class TOPPIDFilter : } } + if (getFlag_("remove_decoys")) + { + LOG_INFO << "Removing decoy hits..." << endl; + IDFilter::removeDecoyHits(peptides); + IDFilter::removeDecoyHits(proteins); + } + // Clean-up: if (!getFlag_("keep_unreferenced_protein_hits")) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index af181c33f27..a0e2d482123 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -2003,10 +2003,37 @@ static void scoreShiftedFragments_( ModifiedPeptideGenerator::applyVariableModifications(variable_modifications.begin(), variable_modifications.end(), aas, max_variable_mods_per_peptide, all_modified_peptides); // reannotate much more memory heavy AASequence object - AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; + AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; ph.setScore(ah.score); ph.setMetaValue(String("RNPxl:score"), ah.score); // important for Percolator feature set because the PeptideHit score might be overwritten by a q-value + // - # of variable mods + // - Phosphopeptide + int is_phospho(0); + int n_var_mods = 0; + for (Size i = 0; i != fixed_and_variable_modified_peptide.size(); ++i) + { + const Residue& r = fixed_and_variable_modified_peptide[i]; + if (!r.isModified()) continue; + if (std::find(variable_modifications.begin(), variable_modifications.end(), *(r.getModification())) != variable_modifications.end()) + { + ++n_var_mods; + } + if (r.getModification()->getId() == "Phospho") { is_phospho = 1; } + } + auto n_term_mod = fixed_and_variable_modified_peptide.getNTerminalModification(); + auto c_term_mod = fixed_and_variable_modified_peptide.getCTerminalModification(); + + if (n_term_mod != nullptr && + std::find(variable_modifications.begin(), variable_modifications.end(), + *n_term_mod) != variable_modifications.end()) ++n_var_mods; + if (c_term_mod != nullptr && + std::find(variable_modifications.begin(), variable_modifications.end(), + *c_term_mod) != variable_modifications.end()) ++n_var_mods; + + ph.setMetaValue(String("variable_modifications"), n_var_mods); + + // determine NA modification from index in map std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, ah.rna_mod_index); @@ -2034,6 +2061,8 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("RNPxl:RNA"), *mod_combinations_it->second.begin()); // return first nucleotide formula matching the index of the empirical formula ph.setMetaValue(String("RNPxl:NT"), String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide ph.setMetaValue(String("RNPxl:RNA_MASS_z0"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight()); // NA uncharged mass via empirical formula + ph.setMetaValue(String("RNPxl:isXL"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight() > 0); + ph.setMetaValue(String("RNPxl:isPhospho"), is_phospho); ph.setMetaValue(String("RNPxl:best_localization_score"), ah.best_localization_score); ph.setMetaValue(String("RNPxl:localization_scores"), ah.localization_scores); @@ -2095,6 +2124,9 @@ static void scoreShiftedFragments_( feature_set << "isotope_error" << "RNPxl:score" + << "variable_modifications" + << "RNPxl:isXL" + << "RNPxl:isPhospho" << "RNPxl:mass_error_p" << "RNPxl:total_loss_score" << "RNPxl:modds" @@ -2271,9 +2303,9 @@ static void scoreShiftedFragments_( auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); ah.ladder_score = ladderScore_(range) / (double)intensity_sum.size(); range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); - if (range.second != range.first) + if (range.second != range.first) // see Macot Percolator paper { - ah.sequence_score = ladderScore_(range) / (double)(range.second - range.first); + ah.sequence_score = ladderScore_(range) / (double)intensity_sum.size(); } // simple combined score in fast scoring: @@ -2799,7 +2831,7 @@ static void scoreShiftedFragments_( range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); if (range.second != range.first) { - ah.sequence_score = ladderScore_(range) / (double)(range.second - range.first); + ah.sequence_score = ladderScore_(range) / (double)intensity_sum.size(); } // combined score @@ -2992,7 +3024,7 @@ static void scoreShiftedFragments_( range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); if (range.second != range.first) { - ah.sequence_score = ladderScore_(range) / (double)(range.second - range.first); + ah.sequence_score = ladderScore_(range) / (double)intensity_sum.size(); } // combined score From a5157f9a8d0c5f005180501b55ab087a8f0b842e Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 20 May 2019 16:00:51 +0200 Subject: [PATCH 041/471] [FIX] add missing OpenMP macro --- src/utils/RNPxlSearch.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index a0e2d482123..5854490e088 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -2232,7 +2232,9 @@ static void scoreShiftedFragments_( const double & fragment_mass_tolerance, const bool & fragment_mass_tolerance_unit_ppm, vector & annotated_hits, +#ifdef _OPENMP omp_lock_t & annotated_hits_lock, +#endif const Size& report_top_hits) { const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); @@ -3080,7 +3082,9 @@ static void scoreShiftedFragments_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, annotated_hits[scan_index], +#ifdef _OPENMP annotated_hits_lock[scan_index], +#endif report_top_hits ); } From f5d75c0008a520c0e8fd4f527650310c2f317355 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Mon, 20 May 2019 15:11:26 +0200 Subject: [PATCH 042/471] [FEATURE] annotate ion index and charge as subscript --- .../ANNOTATION/Annotation1DPeakItem.cpp | 68 +++++++++++++++++-- 1 file changed, 63 insertions(+), 5 deletions(-) diff --git a/src/openms_gui/source/VISUAL/ANNOTATION/Annotation1DPeakItem.cpp b/src/openms_gui/source/VISUAL/ANNOTATION/Annotation1DPeakItem.cpp index 35ee62102ee..132fe265952 100644 --- a/src/openms_gui/source/VISUAL/ANNOTATION/Annotation1DPeakItem.cpp +++ b/src/openms_gui/source/VISUAL/ANNOTATION/Annotation1DPeakItem.cpp @@ -196,20 +196,78 @@ namespace OpenMS painter.setPen(Qt::DashLine); if (!found_intersection) // no intersection with bounding box of text -> normal drawing { - painter.drawLine(peak_position_widget, position_widget); - painter.drawLine(peak_position_widget, position_widget); + painter.drawLine(peak_position_widget, peak_position_widget + QPoint(0, vertical_shift)); + painter.drawLine(peak_position_widget + QPoint(0, vertical_shift), position_widget); } else { - painter.drawLine(peak_position_widget, *closest_ip); - painter.drawLine(peak_position_widget, *closest_ip); + QPoint vertical_end = QPoint(peak_position_widget.x(), position_widget.y() + 20); + + if (vertical_end.y() < peak_position_widget.y()) // label is above peak + { + painter.drawLine(peak_position_widget, vertical_end); + painter.drawLine(vertical_end, position_widget); + } + else // label is below peak + { + painter.drawLine(peak_position_widget, *closest_ip); + painter.drawLine(peak_position_widget, *closest_ip); + } } painter.restore(); delete(ip); delete(closest_ip); } - painter.drawText(bounding_box_, Qt::AlignCenter, text_); + // some pretty printing + QString text = text_; + if (!text.contains("<\\")) // don't process HTML strings again + { + // extract ion index + QRegExp reg_exp("[a|b|c|x|y|z](\\d+)"); + int match_pos = reg_exp.indexIn(text); + if (match_pos == 0) + { + QString index_str = reg_exp.cap(1); + + // put sub html tag around number + text = text[0] + + QString("") + index_str + QString("") + + text.right(text.size() - match_pos - index_str.size() - 1); + } + + // charge + text.replace(QRegExp("3\\+$"), "3+"); + text.replace(QRegExp("\\+\\+$"), "2+"); + text.replace(QRegExp("\\+$"), ""); + text.replace(QRegExp("3\\-$"), "3-"); + text.replace(QRegExp("\\-\\-$"), "2-"); + text.replace(QRegExp("\\-$"), ""); + + // common losses + text.replace("H2O","H2O"); + text.replace("H2O1","H2O"); + text.replace("NH3","NH3"); + text.replace("H3N1","NH3"); + + // nucleotide XL realted losses + text.replace("H3PO4","H3PO4"); + text.replace("HPO3","HPO3"); + text.replace("C3O","C3O"); + } + + QTextDocument td; + td.setHtml(text); + + //draw html text + painter.save(); + double w = td.size().width(); + double h = td.size().height(); + painter.translate(position_widget.x() - w/2, position_widget.y() - h); + td.drawContents(&painter); + painter.restore(); + + //painter.drawText(bounding_box_, Qt::AlignCenter, text_); if (selected_) { drawBoundingBox_(painter); } painter.restore(); From 6feca63373951c1c2b4e7025edc36378a62ef0c0 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 21 May 2019 19:04:32 +0200 Subject: [PATCH 043/471] update tests --- src/tests/topp/RNPxlSearch_1_output.idXML | 1610 ++++++++------ src/tests/topp/RNPxlSearch_2_output.idXML | 1650 ++++++++------ src/tests/topp/RNPxlSearch_3_output.idXML | 2012 +++++++++-------- src/tests/topp/RNPxlSearch_3_output2.tsv | 52 +- src/tests/topp/RNPxlSearch_4_output.idXML | 2472 +++++++++++---------- src/tests/topp/RNPxlSearch_4_output2.tsv | 62 +- src/tests/topp/RNPxlSearch_5_output.idXML | 1686 +++++++------- 7 files changed, 5119 insertions(+), 4425 deletions(-) diff --git a/src/tests/topp/RNPxlSearch_1_output.idXML b/src/tests/topp/RNPxlSearch_1_output.idXML index 012cb77b628..2416eade67a 100644 --- a/src/tests/topp/RNPxlSearch_1_output.idXML +++ b/src/tests/topp/RNPxlSearch_1_output.idXML @@ -4,965 +4,1165 @@ - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - 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b/src/tests/topp/RNPxlSearch_2_output.idXML @@ -4,985 +4,1185 @@ - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - + + + + + + + + + + + + - - - - - - + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - + diff --git a/src/tests/topp/RNPxlSearch_3_output2.tsv b/src/tests/topp/RNPxlSearch_3_output2.tsv index 28ec5b91e1d..254031e7abf 100644 --- a/src/tests/topp/RNPxlSearch_3_output2.tsv +++ b/src/tests/topp/RNPxlSearch_3_output2.tsv @@ -1,28 +1,24 @@ -#RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.06231 A_330.06033 C_112.05108 C_306.0491 G_152.05723 G_346.05525 U_113.03509 U_307.03311 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank -17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 9.6503963470459 3.3154616355896 0 0 16.86 0 0 7.87 0 0 0 331.55 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 -17.788 712.7828 Cas6e UU-H2O1 LRANPIK 2 0.090246170759201 0 0 0 0 0 0 0 0 LRANPIK 810.5076 612.0506 1422.5582 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.4965 697.0 1423.5655 712.2864 475.1933 356.6468 2 -18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.6882381439209 2.21110057830811 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 -25.116 508.1855 Cas5 AU YTPYLGR 3 2.29488754272461 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 -26.237 678.2844 Cas5 U DYHTVLGAR 2 12.8916025161743 0.669801533222198 0 5.20 66.98 0 38.44 0 0 0 0 DYhTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 -26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 18.4397106170654 0.31447559595108 31.45 27.71 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 -26.413 791.8590 Cas5 CU-H2O1-H1O3P1 MRSYLILR 2 0.113397143781185 0 0 0 0 0 0 0 0 0 MRSYLILR 1050.6008 531.1003 1581.7011 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0012 1.5 1582.7084 791.8578 528.2410 396.4325 2 -28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.0663547515869 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 -28.487 828.6961 Cas5 CU-H2O1-H1O3P1 DDTSSLQALSESVQFAVR 3 1.20592641830444 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 DDTSSLQALSESVQFAVR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 -28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.97541213035583 0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 -31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 11.8183317184448 4.78818416595459 0 0 0 0 0 21.64 0 0 0 478.82 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 -31.812 957.3968 Cse2 GU-H2O1-H1O3P1 LVQPFGWENPR 2 0.747869372367859 0 0 0 0 0 0 0 0 0 0 0 0 LVQPFGWENPR 1341.6830 571.1064 1912.7894 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 0.0052 -5.4 1913.7967 957.4020 638.6037 479.2046 2 -33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74868535995483 3.94590377807617 0 0 394.59 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 -33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 9.35625553131104 0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 -34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7075061798096 3.29842972755432 329.84 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 -34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 6.52631330490112 0.941199779510498 0 0 0 94.12 0 0 0 0 0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 -34.072 648.2559 Cas5 UU-H2O1 AVLKPR 2 0.14242060482502 0 0 0 0 0 0 0 AVLKPR 682.4490 612.0506 1294.4996 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0012 -1.8 1295.5069 648.2571 432.5071 324.6322 2 -36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 15.1146411895752 2.23655247688293 0 0 0 0 0 0 223.66 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 -36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 9.68333625793457 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 -37.098 735.8139 Cse1 U ALYTFAEGFK 2 15.285400390625 1.49806451797485 16.33 0 0 88.31 118.17 130.54 0 149.81 138.77 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 -37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.49998235702515 4.44108915328979 0 0 0 0 0 0 444.11 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 -37.864 698.2974 Cas5 U DEPMITLPR 2 10.3271074295044 0.301817148923874 0 0 30.18 0 0 0 0 17.27 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 -37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 0.245834589004517 0 0 0 0 0 0 0 0 GNIKRCR 845.4654 549.1108 1394.5762 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 -37.864 698.2974 Cas7 CU-H2O1-H1O3P1 DAIFGGKR 2 0.214921742677689 0 0 0 0 0 0 0 0 0 DAIFGGKR 862.4661 531.1003 1393.5664 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.5069 726.4 1394.5736 697.7905 465.5294 349.3989 3 -39.118 623.2540 Cse2 U MLTWWGK 2 3.63289213180542 1.09774243831635 0 0 0 109.77 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 -39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 9.60610485076904 1.2768223285675 0 0 0 0 0 0 0 0 127.68 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 -40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 4.67635536193848 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 +#RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank +17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 7.534770011901856 3.3154616355896 0 0 16.86 0 0 7.87 0 0 0 331.55 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 +18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 1.020841717720032 2.211100578308105 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 +25.116 508.1855 Cas5 AU YTPYLGR 3 1.766234636306763 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 +26.237 678.2844 Cas5 U DYHTVLGAR 2 10.246984481811523 0.669801533222199 0 5.20 66.98 0 38.44 0 0 0 0 DYhTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 +26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 11.271114349365234 0.31447559595108 31.45 27.71 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 +28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 7.450744152069092 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 +28.487 828.6961 Cas5 CU-H2O1-H1O3P1 DDTSSLQALSESVQFAVR 3 -4.732399463653565 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 DDTSSLQALSESVQFAVR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 +28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.044219493865967 0.0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 +31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.911904335021973 4.414139270782471 0 0 0 0 0 0 0 0 0 441.41 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 +31.812 957.3968 Cse2 GU-H2O1-H1O3P1 LVQPFGWENPR 2 -4.426882266998291 0.0 0 0 0 0 0 0 0 0 0 0 0 LVQPFGWENPR 1341.6830 571.1064 1912.7894 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 0.0052 -5.4 1913.7967 957.4020 638.6037 479.2046 2 +33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.043148756027222 3.945903778076172 0 0 394.59 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 +33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 4.868203163146973 0.0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 +34.016 790.8062 Cas7 U MATSGMMTELGK 2 11.939115524291992 3.298429727554321 329.84 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 +34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 3.889295816421509 0.941199779510498 0 0 0 94.12 0 0 0 0 0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 +36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 9.927228927612305 2.236552476882935 0 0 0 0 0 0 223.66 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 +36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 5.632431030273438 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 +37.098 735.8139 Cse1 U ALYTFAEGFK 2 11.312786102294922 1.498064517974854 16.33 0 0 88.31 118.17 130.54 0 149.81 138.77 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 +37.536 833.8672 Cse2 U LVQPFGWENPR 2 3.501814842224121 4.441089153289795 0 0 0 0 0 0 444.11 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 +37.864 698.2974 Cas5 U DEPMITLPR 2 6.724847316741943 0.301817148923874 0 0 30.18 0 0 0 0 17.27 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 +37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 -3.122588157653809 0.0 0 0 0 0 0 0 0 GNIKRCR 845.4654 549.1108 1394.5762 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 +39.118 623.2540 Cse2 U MLTWWGK 2 3.027589559555054 1.054794073104858 0 0 0 105.48 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 +39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 4.12628173828125 1.066928863525391 0 0 0 0 0 0 0 0 106.69 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 +40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 -1.674614667892456 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 diff --git a/src/tests/topp/RNPxlSearch_4_output.idXML b/src/tests/topp/RNPxlSearch_4_output.idXML index 1ccf1553d3a..2901065f7af 100644 --- a/src/tests/topp/RNPxlSearch_4_output.idXML +++ b/src/tests/topp/RNPxlSearch_4_output.idXML @@ -4,1525 +4,1629 @@ - + - + - + - + - - + + - - + + - + - + - - + + - - + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + - - - - - - - - - - + + + + + + + + + + + + - - - - - - + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - - - + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + - - - - - - + + + + + + + + + - - - - - - - - - - + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - + + + + + + + + - - - - - - - - - - + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + diff --git a/src/tests/topp/RNPxlSearch_4_output2.tsv b/src/tests/topp/RNPxlSearch_4_output2.tsv index 317278a6a64..44075ee16cd 100644 --- a/src/tests/topp/RNPxlSearch_4_output2.tsv +++ b/src/tests/topp/RNPxlSearch_4_output2.tsv @@ -1,33 +1,29 @@ -#RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.06231 A_330.06033 C_112.05108 C_306.0491 G_152.05723 G_346.05525 U_113.03509 U_307.03311 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank -17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 9.6503963470459 3.3154616355896 0 0 16.86 0 0 7.87 0 0 0 331.55 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 -17.788 712.7828 DECOY_Cas7 U-H2O1 KDDLNDAEAK 2 1.92950487136841 0.277454644441605 27.75 25.43 22.99 0 0 0 0 0 0 0 kDDLNDAEAK 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 2 -18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 2.6882381439209 2.21110057830811 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 -25.116 508.1855 Cas5 AU YTPYLGR 3 2.29488754272461 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 -26.237 678.2844 Cas5 U DYHTVLGAR 2 12.8916025161743 0.669801533222198 0 5.20 66.98 0 38.44 0 0 0 0 DYhTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 -26.237 678.2844 DECOY_Cas5 U AGLVTHYDR 2 0.30169016122818 0.0519835986196995 0 0 0 0 0 0 5.20 0 0 AGLVTHyDR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 2 -26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 18.4397106170654 0.31447559595108 31.45 27.71 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 -26.413 791.8590 DECOY_Cas7 U-H2O1 QDFREGLKQR 2 0.862544894218445 0 0 0 0 0 0 0 0 0 0 0 QDFREGLKQR 1275.6684 306.0253 1581.6937 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0049 6.2 1582.7010 791.8541 528.2385 396.4307 2 -28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.0663547515869 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 -28.487 828.6961 DECOY_Cas5 CU-H2O1-H1O3P1 VAFQVSESLAQLSSTDDR 3 1.21134221553802 1.08878767490387 108.88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 vAFQVSESLAQLSSTDDR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 -28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.97541213035583 0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 -31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 11.8183317184448 4.78818416595459 0 0 0 0 0 21.64 0 0 0 478.82 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 -31.812 957.3968 DECOY_Cse2 U IQACSGNDLQQWAR 2 1.4375159740448 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 IQACSGNDLQQWAR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 2 -33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.74868535995483 3.94590377807617 0 0 394.59 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 -33.237 510.2805 DECOY_Cas7 U-H2O1 LVKLLK 2 1.40665316581726 1.04094266891479 0 0 104.09 0 0 0 LVkLLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 -33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 9.35625553131104 0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 -34.016 790.8062 Cas7 U MATSGMMTELGK 2 19.7075061798096 3.29842972755432 329.84 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 -34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 6.52631330490112 0.941199779510498 0 0 0 94.12 0 0 0 0 0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 -34.072 648.2559 Cas5 UU-H2O1 AVLKPR 2 0.14242060482502 0 0 0 0 0 0 0 AVLKPR 682.4490 612.0506 1294.4996 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0012 -1.8 1295.5069 648.2571 432.5071 324.6322 2 -36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 15.1146411895752 2.23655247688293 0 0 0 0 0 0 223.66 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 -36.528 938.3693 DECOY_Cse1 AU-H2O1 GNSPGGQPKLER 2 0.225188031792641 0 0 0 0 0 0 0 0 0 0 0 0 0 GNSPGGQPKLER 1238.6368 635.0778 1873.7146 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.5047 538.1 1874.7219 937.8646 625.5788 469.4359 2 -36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 9.68333625793457 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 -36.767 933.9406 DECOY_Cas7 U-H2O1 EAEDVSKGSLLALTK 2 0.209372878074646 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 EAEDVSKGSLLALTK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 2 -37.098 735.8139 Cse1 U ALYTFAEGFK 2 15.285400390625 1.49806451797485 16.33 0 0 88.31 118.17 130.54 0 149.81 138.77 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 -37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 0.321959912776947 0 0 0 0 0 0 0 0 0 0 0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 -37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.49998235702515 4.44108915328979 0 0 0 0 0 0 444.11 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 -37.864 698.2974 Cas5 U DEPMITLPR 2 10.3271074295044 0.301817148923874 0 0 30.18 0 0 0 0 17.27 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 -37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 0.245834589004517 0 0 0 0 0 0 0 0 GNIKRCR 845.4654 549.1108 1394.5762 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 -39.118 623.2540 Cse2 U MLTWWGK 2 3.63289213180542 1.09774243831635 0 0 0 109.77 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 -39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 9.60610485076904 1.2768223285675 0 0 0 0 0 0 0 0 127.68 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 -39.853 861.3889 DECOY_Cas5 U GTPRTGEFTPQGWAQMPGALR 3 2.99445772171021 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 GTPRTGEFTPQGWAQMPGALR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 2 -40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 4.67635536193848 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 +#RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank +17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 7.534770011901856 3.3154616355896 0 0 16.86 0 0 7.87 0 0 0 331.55 AEADNLDDKk 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 +17.788 712.7828 DECOY_Cas7 U-H2O1 KDDLNDAEAK 2 0.540192306041718 0.247234299778938 0 24.72 22.28 0 0 9.75 0 0 0 0 KdDLNDAEAK 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 2 +18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 1.020841717720032 2.211100578308105 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 +25.116 508.1855 Cas5 AU YTPYLGR 3 1.766234636306763 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 +26.237 678.2844 Cas5 U DYHTVLGAR 2 10.246984481811523 0.669801533222199 0 5.20 66.98 0 38.44 0 0 0 0 DYhTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 +26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 11.271114349365234 0.31447559595108 31.45 27.71 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 +26.413 791.8590 DECOY_Cas7 U-H2O1 QDFREGLKQR 2 -4.288217067718506 0.0 0 0 0 0 0 0 0 0 0 0 QDFREGLKQR 1275.6684 306.0253 1581.6937 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0049 6.2 1582.7010 791.8541 528.2385 396.4307 2 +28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 7.450744152069092 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 +28.487 828.6961 DECOY_Cas5 CU-H2O1-H1O3P1 VAFQVSESLAQLSSTDDR 3 -4.445086002349854 1.08878767490387 108.88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 vAFQVSESLAQLSSTDDR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 +28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.044219493865967 0.0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 +31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.911904335021973 4.414139270782471 0 0 0 0 0 0 0 0 0 441.41 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 +31.812 957.3968 DECOY_Cse2 U IQACSGNDLQQWAR 2 -0.950542509555817 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 IQACSGNDLQQWAR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 2 +33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.043148756027222 3.945903778076172 0 0 394.59 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 +33.237 510.2805 DECOY_Cas7 U-H2O1 LVKLLK 2 -0.157985359430313 1.040942668914795 0 0 104.09 0 0 0 LVkLLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 +33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 4.868203163146973 0.0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 +34.016 790.8062 Cas7 U MATSGMMTELGK 2 11.939115524291992 3.298429727554321 329.84 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 +34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 3.889295816421509 0.941199779510498 0 0 0 94.12 0 0 0 0 0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 +36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 9.927228927612305 2.236552476882935 0 0 0 0 0 0 223.66 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 +36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 5.632431030273438 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 +37.098 735.8139 Cse1 U ALYTFAEGFK 2 11.312786102294922 1.498064517974854 16.33 0 0 88.31 118.17 130.54 0 149.81 138.77 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 +37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 -2.599616527557373 0.0 0 0 0 0 0 0 0 0 0 0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 +37.536 833.8672 Cse2 U LVQPFGWENPR 2 3.501814842224121 4.441089153289795 0 0 0 0 0 0 444.11 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 +37.864 698.2974 Cas5 U DEPMITLPR 2 6.724847316741943 0.301817148923874 0 0 30.18 0 0 0 0 17.27 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 +37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 -3.122588157653809 0.0 0 0 0 0 0 0 0 GNIKRCR 845.4654 549.1108 1394.5762 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 +39.118 623.2540 Cse2 U MLTWWGK 2 3.027589559555054 1.054794073104858 0 0 0 105.48 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 +39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 4.12628173828125 1.066928863525391 0 0 0 0 0 0 0 0 106.69 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 +39.853 861.3889 DECOY_Cas5 U GTPRTGEFTPQGWAQMPGALR 3 0.42877921462059 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 GTPRTGEFTPQGWAQMPGALR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 2 +40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 -1.674614667892456 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 diff --git a/src/tests/topp/RNPxlSearch_5_output.idXML b/src/tests/topp/RNPxlSearch_5_output.idXML index 494fd2d3e6f..dfb4b0ef385 100644 --- a/src/tests/topp/RNPxlSearch_5_output.idXML +++ b/src/tests/topp/RNPxlSearch_5_output.idXML @@ -4,1042 +4,1182 @@ - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - - + + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - + + + + + + + + + + - - - - - - + + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - + + + - - - - - - - + + + + + + + + - - - - - - - - + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - - - + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - - - - - - - + + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - - - + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + From 198a0e4efa5486f8a5ef7ebee11c1708b97b1d46 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 21 May 2019 19:20:18 +0200 Subject: [PATCH 044/471] some test fixes --- .../TheoreticalSpectrumGenerator_test.cpp | 120 +++++++++--------- src/utils/RNPxlSearch.cpp | 2 +- 2 files changed, 61 insertions(+), 61 deletions(-) diff --git a/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp b/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp index 0221cdf24e9..49fc4abf572 100644 --- a/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp +++ b/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp @@ -180,42 +180,42 @@ START_SECTION(void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, In TEST_EQUAL(spec.size(), 30) set ion_names; // ions without losses - ion_names.insert("b1+"); - ion_names.insert("x1+"); - ion_names.insert("b2+"); - ion_names.insert("x2+"); - ion_names.insert("b3+"); - ion_names.insert("x3+"); - ion_names.insert("b4+"); - ion_names.insert("x4+"); - ion_names.insert("b5+"); - ion_names.insert("x5+"); - ion_names.insert("b6+"); - ion_names.insert("x6+"); + ion_names.insert("b1"); + ion_names.insert("x1"); + ion_names.insert("b2"); + ion_names.insert("x2"); + ion_names.insert("b3"); + ion_names.insert("x3"); + ion_names.insert("b4"); + ion_names.insert("x4"); + ion_names.insert("b5"); + ion_names.insert("x5"); + ion_names.insert("b6"); + ion_names.insert("x6"); // currently losses are generated independent of ion ladder type (b,y,...) // if an amino acid with potential loss is present in the prefix/suffix, then the loss is applied // if multiple amino acids with the same e.g. water loss are present in the prefix/suffix ion then the loss is only applied once - ion_names.insert("x1-H3N1+"); - ion_names.insert("x2-H3N1+"); - ion_names.insert("x3-H3N1+"); - ion_names.insert("b3-H2O1+"); - ion_names.insert("x4-H3N1+"); - ion_names.insert("b4-H2O1+"); - ion_names.insert("b4-H3N1+"); - ion_names.insert("x5-H2O1+"); - ion_names.insert("x5-H3N1+"); - ion_names.insert("b5-H2O1+"); - ion_names.insert("b5-H3N1+"); - ion_names.insert("b6-H2O1+"); - ion_names.insert("b6-H3N1+"); - ion_names.insert("x6-H2O1+"); - ion_names.insert("x6-H3N1+"); + ion_names.insert("x1-H3N1"); + ion_names.insert("x2-H3N1"); + ion_names.insert("x3-H3N1"); + ion_names.insert("b3-H2O1"); + ion_names.insert("x4-H3N1"); + ion_names.insert("b4-H2O1"); + ion_names.insert("b4-H3N1"); + ion_names.insert("x5-H2O1"); + ion_names.insert("x5-H3N1"); + ion_names.insert("b5-H2O1"); + ion_names.insert("b5-H3N1"); + ion_names.insert("b6-H2O1"); + ion_names.insert("b6-H3N1"); + ion_names.insert("x6-H2O1"); + ion_names.insert("x6-H3N1"); // precursors - ion_names.insert("[M+H]-H2O+"); - ion_names.insert("[M+H]-NH3+"); - ion_names.insert("[M+H]+"); + ion_names.insert("[M+H]-H2O"); + ion_names.insert("[M+H]-NH3"); + ion_names.insert("[M+H]"); PeakSpectrum::StringDataArray string_array = spec.getStringDataArrays().at(0); @@ -247,42 +247,42 @@ START_SECTION(void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, In ion_names.clear(); // ions without losses - ion_names.insert("b1+++"); - ion_names.insert("x1+++"); - ion_names.insert("b2+++"); - ion_names.insert("x2+++"); - ion_names.insert("b3+++"); - ion_names.insert("x3+++"); - ion_names.insert("b4+++"); - ion_names.insert("x4+++"); - ion_names.insert("b5+++"); - ion_names.insert("x5+++"); - ion_names.insert("b6+++"); - ion_names.insert("x6+++"); + ion_names.insert("b1"); + ion_names.insert("x1"); + ion_names.insert("b2"); + ion_names.insert("x2"); + ion_names.insert("b3"); + ion_names.insert("x3"); + ion_names.insert("b4"); + ion_names.insert("x4"); + ion_names.insert("b5"); + ion_names.insert("x5"); + ion_names.insert("b6"); + ion_names.insert("x6"); // currently losses are generated independent of ion ladder type (b,y,...) // if an amino acid with potential loss is present in the prefix/suffix, then the loss is applied // if multiple amino acids with the same e.g. water loss are present in the prefix/suffix ion then the loss is only applied once - ion_names.insert("x1-H3N1+++"); - ion_names.insert("x2-H3N1+++"); - ion_names.insert("x3-H3N1+++"); - ion_names.insert("b3-H2O1+++"); - ion_names.insert("x4-H3N1+++"); - ion_names.insert("b4-H2O1+++"); - ion_names.insert("b4-H3N1+++"); - ion_names.insert("x5-H2O1+++"); - ion_names.insert("x5-H3N1+++"); - ion_names.insert("b5-H2O1+++"); - ion_names.insert("b5-H3N1+++"); - ion_names.insert("b6-H2O1+++"); - ion_names.insert("b6-H3N1+++"); - ion_names.insert("x6-H2O1+++"); - ion_names.insert("x6-H3N1+++"); + ion_names.insert("x1-H3N1"); + ion_names.insert("x2-H3N1"); + ion_names.insert("x3-H3N1"); + ion_names.insert("b3-H2O1"); + ion_names.insert("x4-H3N1"); + ion_names.insert("b4-H2O1"); + ion_names.insert("b4-H3N1"); + ion_names.insert("x5-H2O1"); + ion_names.insert("x5-H3N1"); + ion_names.insert("b5-H2O1"); + ion_names.insert("b5-H3N1"); + ion_names.insert("b6-H2O1"); + ion_names.insert("b6-H3N1"); + ion_names.insert("x6-H2O1"); + ion_names.insert("x6-H3N1"); // precursors - ion_names.insert("[M+H]-H2O+++"); - ion_names.insert("[M+H]-NH3+++"); - ion_names.insert("[M+H]+++"); + ion_names.insert("[M+H]-H2O"); + ion_names.insert("[M+H]-NH3"); + ion_names.insert("[M+H]"); string_array = spec.getStringDataArrays().at(0); diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 10f7a67f1b7..5fc66165aa6 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -108,7 +108,7 @@ using namespace std; // stores which residues (known to give rise to immonium ions) are in the sequence struct ImmoniumIonsInPeptide { - ImmoniumIonsInPeptide(const String& s) + explicit ImmoniumIonsInPeptide(const String& s) { for (const char & c : s) { From b2e83fae93aa5c9aae38593d1490cc414fc0e99a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 22 May 2019 14:13:06 +0200 Subject: [PATCH 045/471] update THIRDPARTY --- THIRDPARTY | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/THIRDPARTY b/THIRDPARTY index 45634c52139..2f9795c1eba 160000 --- a/THIRDPARTY +++ b/THIRDPARTY @@ -1 +1 @@ -Subproject commit 45634c521396120cf9b50adf859564e17e3e44b9 +Subproject commit 2f9795c1ebad57b6118aafbefc53b19159ebaab4 From 1de3de5f4addc05fea235ba62ea67d4c5e302d89 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 22 May 2019 15:35:49 +0200 Subject: [PATCH 046/471] fix tests --- .../source/CHEMISTRY/SpectrumAnnotator.cpp | 8 ++++---- .../openms/source/SpectrumAnnotator_test.cpp | 4 ++-- .../TheoreticalSpectrumGenerator_test.cpp | 20 +++++++++++++------ 3 files changed, 20 insertions(+), 12 deletions(-) diff --git a/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp b/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp index efe2428b5d6..40f2e85333b 100644 --- a/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp +++ b/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp @@ -41,10 +41,10 @@ using namespace std; namespace OpenMS { - const boost::regex SpectrumAnnotator::nt_regex_("[a,b,c][[:digit:]]+[+]+"); - const boost::regex SpectrumAnnotator::ct_regex_("[x,y,z][[:digit:]]+[+]+"); - const boost::regex SpectrumAnnotator::noloss_regex_("[a,b,c,x,y,z][[:digit:]]+[+]+"); - const boost::regex SpectrumAnnotator::seriesposition_regex_("[a,b,c,x,y,z]([[:digit:]]+)[+,-]+[[:word:]]*[+]*"); + const boost::regex SpectrumAnnotator::nt_regex_("[a,b,c][[:digit:]]+[+]*"); + const boost::regex SpectrumAnnotator::ct_regex_("[x,y,z][[:digit:]]+[+]*"); + const boost::regex SpectrumAnnotator::noloss_regex_("[a,b,c,x,y,z][[:digit:]]+[+]*"); + const boost::regex SpectrumAnnotator::seriesposition_regex_("[a,b,c,x,y,z]([[:digit:]]+)[+,-]*[[:word:]]*[+]*"); SpectrumAnnotator::SpectrumAnnotator() : DefaultParamHandler("SpectrumAnnotator") diff --git a/src/tests/class_tests/openms/source/SpectrumAnnotator_test.cpp b/src/tests/class_tests/openms/source/SpectrumAnnotator_test.cpp index 2c22dc41bf7..3d578c36517 100644 --- a/src/tests/class_tests/openms/source/SpectrumAnnotator_test.cpp +++ b/src/tests/class_tests/openms/source/SpectrumAnnotator_test.cpp @@ -94,7 +94,7 @@ pi.setHits(std::vector(1,hit)); START_SECTION((void SpectrumAnnotator::annotateMatches(PeakSpectrum& spec, const PeptideHit& ph, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const)) annot.annotateMatches(spec, hit, tg, sa); - string annotlist[] = {"y1+", "y2+", "b2+", "y3+", "b3+", "y4+", "b4+", "y5+", "b5+", "b6+", "y6+"}; + string annotlist[] = {"y1", "y2", "b2", "y3", "b3", "y4", "b4", "y5", "b5", "b6", "y6"}; PeakSpectrum::StringDataArray types = spec.getStringDataArrays().front(); @@ -115,7 +115,7 @@ START_SECTION((void SpectrumAnnotator::addIonMatchStatistics(PeptideIdentificati TEST_EQUAL(pi.getHits()[i].getMetaValue("sum_intensity"),12.1) TEST_EQUAL(pi.getHits()[i].getMetaValue("matched_ion_number"),11) TEST_EQUAL(pi.getHits()[i].getMetaValue("matched_intensity"),12.1) - TEST_STRING_EQUAL(pi.getHits()[i].getMetaValue("matched_ions"),"y1+,y2+,b2+,y3+,b3+,y4+,b4+,y5+,b5+,b6+,y6+") + TEST_STRING_EQUAL(pi.getHits()[i].getMetaValue("matched_ions"),"y1,y2,b2,y3,b3,y4,b4,y5,b5,b6,y6") TEST_STRING_EQUAL(pi.getHits()[i].getMetaValue("max_series_type"),"y") TEST_EQUAL(pi.getHits()[i].getMetaValue("max_series_size"),6) TEST_REAL_SIMILAR(pi.getHits()[i].getMetaValue("sn_by_matched_intensity"),0) diff --git a/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp b/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp index 49fc4abf572..532095ca2e1 100644 --- a/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp +++ b/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp @@ -213,8 +213,8 @@ START_SECTION(void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, In ion_names.insert("x6-H3N1"); // precursors - ion_names.insert("[M+H]-H2O"); - ion_names.insert("[M+H]-NH3"); + ion_names.insert("[M+H-H2O]"); + ion_names.insert("[M+H-NH3]"); ion_names.insert("[M+H]"); PeakSpectrum::StringDataArray string_array = spec.getStringDataArrays().at(0); @@ -223,7 +223,11 @@ START_SECTION(void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, In for (Size i = 0; i != spec.size(); ++i) { String name = string_array[i]; - TEST_EQUAL(ion_names.find(name) != ion_names.end(), true) + if (ion_names.find(name) == ion_names.end()) + { + std::cout << "Test Error: " << name << " not found." << std::endl; + } + TEST_EQUAL(ion_names.find(name) != ion_names.end(), true); } // test for charges stored in IntegerDataArray @@ -280,9 +284,9 @@ START_SECTION(void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, In ion_names.insert("x6-H3N1"); // precursors - ion_names.insert("[M+H]-H2O"); - ion_names.insert("[M+H]-NH3"); - ion_names.insert("[M+H]"); + ion_names.insert("[M+3H-H2O]"); + ion_names.insert("[M+3H-NH3]"); + ion_names.insert("[M+3H]"); string_array = spec.getStringDataArrays().at(0); @@ -290,6 +294,10 @@ START_SECTION(void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, In for (Size i = 0; i != spec.size(); ++i) { String name = string_array[i]; + if (ion_names.find(name) == ion_names.end()) + { + std::cout << "Test Error: " << name << " not found." << std::endl; + } TEST_EQUAL(ion_names.find(name) != ion_names.end(), true) } From 72b5bae60a2d998b4eb85b7d98ebccb151dbe9d3 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 22 May 2019 16:19:16 +0200 Subject: [PATCH 047/471] fix some linter --- src/openms/source/CHEMISTRY/Tagger.cpp | 2 +- src/utils/RNPxlSearch.cpp | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/openms/source/CHEMISTRY/Tagger.cpp b/src/openms/source/CHEMISTRY/Tagger.cpp index 8ba8baaeb80..998fe46b9fe 100644 --- a/src/openms/source/CHEMISTRY/Tagger.cpp +++ b/src/openms/source/CHEMISTRY/Tagger.cpp @@ -76,7 +76,7 @@ namespace OpenMS min_tag_length_ = min_tag_length; max_tag_length_ = max_tag_length; const std::set aas = ResidueDB::getInstance()->getResidues(); - for (auto r : aas) + for (const auto & r : aas) { const char letter = r->getOneLetterCode()[0]; const float mass = r->getMonoWeight(Residue::Internal); diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index 5fc66165aa6..3192c1c4560 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -112,7 +112,7 @@ struct ImmoniumIonsInPeptide { for (const char & c : s) { - switch(c) + switch (c) { case 'Y': Y = true; break; case 'W': W = true; break; @@ -488,8 +488,8 @@ class RNPxlSearch : { const double intensity = exp_spectrum[index].getIntensity(); b_mean_err += intensity * std::abs(theo_mz - exp_mz); - dot_product += intensity ; - b_ions[i] += intensity ; + dot_product += intensity; + b_ions[i] += intensity; } } } @@ -723,8 +723,8 @@ class RNPxlSearch : { const double intensity = exp_spectrum[index].getIntensity(); b_mean_err += intensity * std::abs(theo_mz - exp_mz); - dot_product += intensity ; - b_ions[i] += intensity ; + dot_product += intensity; + b_ions[i] += intensity; } } } @@ -1235,7 +1235,7 @@ static void scoreShiftedFragments_( vector partial_loss_modification; for (auto const & nuc_2_adducts : feasible_MS2_adducts) { - if(nuc_2_adducts.first == ah.cross_linked_nucleotide) + if (nuc_2_adducts.first == ah.cross_linked_nucleotide) { partial_loss_modification = nuc_2_adducts.second; } @@ -2403,7 +2403,7 @@ static void scoreShiftedFragments_( { int max_l = 0; Iterator best_start(b); - for(auto i = b; i != e;) // iterate once over vector + for (auto i = b; i != e;) // iterate once over vector { for (; i != e && *i <= 0.0; ++i) {}; // skip zeros if (i == e) // end? From 2522e4c1ba84c91b29aced1f363fdf54b3212b31 Mon Sep 17 00:00:00 2001 From: Hannes Roest Date: Tue, 28 May 2019 10:33:27 -0400 Subject: [PATCH 048/471] [FIX] docu fix --- .../OpenMS/ANALYSIS/ID/PrecursorPurity.h | 4 +- .../MAPMATCHING/TransformationDescription.h | 2 +- .../MRM/ReactionMonitoringTransition.h | 4 +- .../OpenMS/ANALYSIS/RNPXL/HyperScore.h | 4 +- .../include/OpenMS/ANALYSIS/RNPXL/PScore.h | 42 ++++++++++++------- .../RNPXL/RNPxlFragmentAnnotationHelper.h | 9 ++-- .../FILTERING/DATAREDUCTION/Deisotoper.h | 2 +- .../METADATA/ID/AppliedProcessingStep.h | 2 +- 8 files changed, 41 insertions(+), 28 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/ID/PrecursorPurity.h b/src/openms/include/OpenMS/ANALYSIS/ID/PrecursorPurity.h index 8a1a6a9ba8e..8861278711f 100644 --- a/src/openms/include/OpenMS/ANALYSIS/ID/PrecursorPurity.h +++ b/src/openms/include/OpenMS/ANALYSIS/ID/PrecursorPurity.h @@ -71,7 +71,7 @@ namespace OpenMS Size residual_peak_count = 0; }; - /* @brief compute precursor purity metrics for each MS2 spectrum in a PeakMap + /** @brief compute precursor purity metrics for each MS2 spectrum in a PeakMap This is the main function of this class. See class description. * @param spectra A PeakMap containing MS1 and MS2 spectra in order of acquisition or measurement. The first spectrum must be an MS1. @@ -80,7 +80,7 @@ namespace OpenMS */ static std::vector computePrecursorPurities(const PeakMap& spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm); - /* @brief compute precursor purity metrics for one MS2 precursor + /** @brief compute precursor purity metrics for one MS2 precursor @note This function is implemented in a general way and can also be used for e.g. MS3 precursor isolation windows in MS2 spectra diff --git a/src/openms/include/OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h b/src/openms/include/OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h index 07487c10a96..7de9285a87d 100644 --- a/src/openms/include/OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h +++ b/src/openms/include/OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h @@ -64,7 +64,7 @@ namespace OpenMS public: - /* @brief Summary statistics before/after applying the transformation. + /** @brief Summary statistics before/after applying the transformation. For deviations before/after transformation, the percentiles 100, 99, 95, 90, 75, 50, 25 are returned. */ diff --git a/src/openms/include/OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h b/src/openms/include/OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h index 814334792e8..3a1ad538a6e 100644 --- a/src/openms/include/OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h +++ b/src/openms/include/OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h @@ -125,7 +125,7 @@ namespace OpenMS void addPrecursorCVTerm(const CVTerm & cv_term); - /* @brief Obtain the list of CV Terms for the precursor + /** @brief Obtain the list of CV Terms for the precursor * * @note You first need to check whether they exist using hasPrecursorCVTerms() */ @@ -158,7 +158,7 @@ namespace OpenMS void addPredictionTerm(const CVTerm & prediction); - /* @brief Obtain the Prediction object + /** @brief Obtain the Prediction object * * @note You first need to check whether the object is accessible using hasPrediction() */ diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h index 11382ca4528..d5f67e31df3 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h @@ -50,7 +50,7 @@ struct OPENMS_DLLAPI HyperScore { typedef std::pair IndexScorePair; - /* @brief compute the (ln transformed) X!Tandem HyperScore + /** @brief compute the (ln transformed) X!Tandem HyperScore * 1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated * 2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions * @note Peak intensities of the theoretical spectrum are typically 1 or TIC normalized, but can also be e.g. ion probabilities @@ -64,7 +64,7 @@ struct OPENMS_DLLAPI HyperScore static double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum); private: - // helper to compute the log factorial + /// helper to compute the log factorial static double logfactorial_(const int x, int base = 2); }; diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/PScore.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/PScore.h index 77c3955d588..58ea5324cd4 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/PScore.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/PScore.h @@ -48,37 +48,48 @@ namespace OpenMS struct OPENMS_DLLAPI PScore { - /* @brief calculate local (windowed) peak ranks. + /** @brief calculate local (windowed) peak ranks. + * * The peak rank is defined as the number of neighboring peaks in +/- (mz_window/2) that have higher intensity * The result can be used to efficiently filter spectra for top 1..n peaks in mass windows - * @note: ranks are zero based (highest intensity peak in window has rank 0) + * + * @note ranks are zero based (highest intensity peak in window has rank 0) + * * @param mz m/z positions of the peaks * @param intensities of the peaks * @param mz_window window in Thomson centered at each peak */ static std::vector calculateIntensityRankInMZWindow(const std::vector& mz, const std::vector& intensities, double mz_window); - /* @brief precalculated, windowed peak ranks for a whole experiment. + /** @brief precalculated, windowed peak ranks for a whole experiment. + * * The peak rank is defined as the number of neighboring peaks in +/- (mz_window/2) that have higher intensity - * 1. Each spectrum is subdivided into windows of size @param mz_window. - * 2. For each window, peak ranks are assigned using calculateIntensityRankInMZWindow. - * 3. A rank map is returned - * @note: ranks are zero based (top element has rank 0) + * + * -# Each spectrum is subdivided into windows of size \p mz_window. + * -# For each window, peak ranks are assigned using calculateIntensityRankInMZWindow(). + * -# A rank map is returned + * + * @note ranks are zero based (top element has rank 0) + * * @param peak_map Fragment spectra used for rank calculation. Typically a peak map after removal of all MS1 spectra. * @param mz_window window in Thomson centered at each peak */ static std::vector > calculateRankMap(const PeakMap& peak_map, double mz_window = 100); - /* @brief Calculates spectra for peak level between min_level to max_level and stores them in the map + /** @brief Calculates spectra for peak level between min_level to max_level and stores them in the map * A spectrum of peak level n retains the (n+1) top intensity peaks in a sliding mz_window centered at each peak. - * @note: levels are zero based (level 0 has only the top intensity peaks for each window, level 1 the top and second most intensive one) - * @note: min and max level are taken from the Andromeda publication but are similar to the AScore publication + * + * @note levels are zero based (level 0 has only the top intensity peaks for each window, level 1 the top and second most intensive one) + * @note min and max level are taken from the Andromeda publication but are similar to the AScore publication + * */ static std::map calculatePeakLevelSpectra(const PeakSpectrum& spec, const std::vector& ranks, Size min_level = 1, Size max_level = 9); - /* @brief Computes the PScore for a vector of theoretical spectra + /** @brief Computes the PScore for a vector of theoretical spectra + * * Similar to Andromeda, a vector of theoretical spectra can be provided that e.g. contain loss spectra or higher charge spectra depending on the sequence. * The best score obtained by scoring all those theoretical spectra against the experimental ones is returned. + * * @param fragment_mass_tolerance mass tolerance for matching peaks * @param fragment_mass_tolerance_unit_ppm whether Thomson or ppm is used * @param peak_level_spectra spectra for different peak levels (=filtered by maximum rank). @@ -87,7 +98,8 @@ struct OPENMS_DLLAPI PScore */ static double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map& peak_level_spectra, const std::vector& theo_spectra, double mz_window = 100.0); - /* @brief Computes the PScore for a single theoretical spectrum + /** @brief Computes the PScore for a single theoretical spectrum + * * @param fragment_mass_tolerance mass tolerance for matching peaks * @param fragment_mass_tolerance_unit_ppm whether Thomson or ppm is used * @param peak_level_spectra spectra for different peak levels (=filtered by maximum rank). @@ -97,15 +109,15 @@ struct OPENMS_DLLAPI PScore static double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map& peak_level_spectra, const PeakSpectrum& theo_spectrum, double mz_window = 100.0); /// additive correction terms used by Andromeda (pscore + massC + cleaveC + modC - 100). For reference see the Andromeda source code. - /// @note: constants used in the correction term might be instrument dependent + /// @note constants used in the correction term might be instrument dependent static double massCorrectionTerm(double mass); /// correction term for type of cleavage. For reference see the Andromeda source code. - /// @note: constants used in the correction term might be instrument dependent + /// @note constants used in the correction term might be instrument dependent static double cleavageCorrectionTerm(Size cleavages, bool consecutive_cleavage); /// correction term for modification. For reference see the Andromeda source code. - /// @note: constants used in the correction term might be instrument dependent + /// @note constants used in the correction term might be instrument dependent static double modificationCorrectionTerm(Size modifications); }; diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h index 17a2720babd..c209eee2d95 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h @@ -49,9 +49,10 @@ namespace OpenMS namespace Internal { -/* @brief Convenience functions to construct appealing fragment annotation strings - * and store them as PeptideHit::PeakAnnotation - * +/** + @brief Convenience functions to construct appealing fragment annotation strings + and store them as PeptideHit::PeakAnnotation + */ class OPENMS_DLLAPI RNPxlFragmentAnnotationHelper { @@ -87,7 +88,7 @@ class OPENMS_DLLAPI RNPxlFragmentAnnotationHelper static String getAnnotatedImmoniumIon(char c, const String& fragment_shift_name); - // conversion of RNPxl annotations to PeptideHit::PeakAnnotation + /// conversion of RNPxl annotations to PeptideHit::PeakAnnotation static std::vector fragmentAnnotationDetailsToPHFA( const String& ion_type, std::map > ion_annotation_details); diff --git a/src/openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h b/src/openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h index eca823f982f..fe9a856389c 100644 --- a/src/openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h +++ b/src/openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h @@ -47,7 +47,7 @@ class OPENMS_DLLAPI Deisotoper { public: - /* @brief Detect isotopic clusters in a fragment spectrum. + /** @brief Detect isotopic clusters in a fragment spectrum. Deisotoping is done in-place and if @p annotate_charge is true, an additional IntegerDataArray "charge" will be appended. diff --git a/src/openms/include/OpenMS/METADATA/ID/AppliedProcessingStep.h b/src/openms/include/OpenMS/METADATA/ID/AppliedProcessingStep.h index 03e785798ab..14eca1bfd92 100644 --- a/src/openms/include/OpenMS/METADATA/ID/AppliedProcessingStep.h +++ b/src/openms/include/OpenMS/METADATA/ID/AppliedProcessingStep.h @@ -69,7 +69,7 @@ namespace OpenMS (scores == other.scores)); } - /* @brief Return scores in order of priority (primary first). + /** @brief Return scores in order of priority (primary first). The order is defined in the @p DataProcessingSoftware referenced by the processing step (if available). Scores not listed there are included at the end of the output. From 596aa6ccaa0fb43b43dd394e901ee3406d86c76c Mon Sep 17 00:00:00 2001 From: Hannes Roest Date: Wed, 29 May 2019 09:11:12 -0400 Subject: [PATCH 049/471] [FEATURE] add "none" model --- .../FILTERING/DATAREDUCTION/Deisotoper.h | 48 ++++++++++++++----- .../FILTERING/DATAREDUCTION/Deisotoper.cpp | 7 ++- src/pyOpenMS/pxds/Deisotoper.pxd | 6 +++ 3 files changed, 48 insertions(+), 13 deletions(-) diff --git a/src/openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h b/src/openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h index fe9a856389c..c554735008b 100644 --- a/src/openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h +++ b/src/openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h @@ -38,6 +38,8 @@ #include #include +#include + namespace OpenMS { @@ -47,28 +49,50 @@ class OPENMS_DLLAPI Deisotoper { public: - /** @brief Detect isotopic clusters in a fragment spectrum. + /** @brief Detect isotopic clusters in a mass spectrum. + + Deisotoping is based on C13 abundance and will try to identify a simple + model based on the C12-C13 distance and charge state. This is often a good + approximation for peptide fragment ion spectra but may not work well for + other spectra. The algorithm will consider each peak (starting from the + right of a spectrum) and, for each peak, attempt to add isotopic peaks to + its envelope until either no peak is found, the maximum number of isotopic + peaks is reached or the intensity of the peak is higher than the previous + peak ("decreasing" model only). Deisotoping is done in-place and if @p annotate_charge is true, an additional IntegerDataArray "charge" will be appended. Existing DataArrays are kept and shrunken to the peaks which remain in the spectrum. - * @param [spectra] Input spectra (sorted by m/z) - * @param [fragment_tolerance] The tolerance used to match isotopic peaks - * @param [fragment_unit_ppm] Whether ppm or m/z is used as tolerance - * @param [min_charge] The minimum charge considered - * @param [max_charge] The maximum charge considered - * @param [keep_only_deisotoped] Only monoisotopic peaks of fragments with isotopic pattern are retained - * @param [min_isopeaks] The minimum number of isotopic peaks (at least 2) required for an isotopic cluster - * @param [max_isopeaks] The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster - * @param [make_single_charged] Convert deisotoped monoisotopic peak to single charge - * @param [annotate_charge] Annotate the charge to the peaks in the IntegerDataArray: "charge" (0 for unknown charge) - * Note: If @p make_single_charged is selected, the original charge (>=1) gets annotated. + @param [spectrum] Input spectra (sorted by m/z) + @param [fragment_tolerance] The tolerance used to match isotopic peaks + @param [fragment_unit_ppm] Whether ppm or m/z is used as tolerance + @param [model] Isotopic model to use (see below) + @param [min_charge] The minimum charge considered + @param [max_charge] The maximum charge considered + @param [keep_only_deisotoped] Only monoisotopic peaks of fragments with isotopic pattern are retained + @param [min_isopeaks] The minimum number of isotopic peaks (at least 2) required for an isotopic cluster + @param [max_isopeaks] The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster + @param [make_single_charged] Convert deisotoped monoisotopic peak to single charge + @param [annotate_charge] Annotate the charge to the peaks in the IntegerDataArray: "charge" (0 for unknown charge) + + @note If @p make_single_charged is selected, the original charge (>=1) gets annotated. + + @note The algorithm expects a centroided spectrum, make sure you have run a peak picker on the data first. + + @note The algorithm only considers C12 and C13 isotopes for the isotopic envelope. + + Available isotopic models: + + - "none": no isotopic model is used and peaks are added to an isotopic envelope even if they are higher in intensity + - "decreasing": the algorithm assumes that the monoisotopic peak is the most abundant peak and all other peaks are lower in intensity (this is a very simplistic model and will only work for low mass ions). This will work for fragment ion spectra of small molecules and peptides, but may not work for other applications. + */ static void deisotopeAndSingleCharge(MSSpectrum& spectrum, double fragment_tolerance, bool fragment_unit_ppm, + std::string model = "decreasing", int min_charge = 1, int max_charge = 3, bool keep_only_deisotoped = false, diff --git a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp index 9ad4acc2b8c..c2b9b714987 100644 --- a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp +++ b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp @@ -46,6 +46,7 @@ namespace OpenMS void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, double fragment_tolerance, bool fragment_unit_ppm, + std::string model, int min_charge, int max_charge, bool keep_only_deisotoped, @@ -55,6 +56,7 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, bool annotate_charge) { OPENMS_PRECONDITION(spec.isSorted(), "Spectrum must be sorted."); + OPENMS_PRECONDITION(model == "decreasing" || model == "none", "Model must be one of: none, decreasing."); if (min_isopeaks < 2 || max_isopeaks < 2 || min_isopeaks > max_isopeaks) { @@ -84,6 +86,9 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, std::vector extensions; + // Decreasing model: assume intensity in the isotopic envelope decreases (this is often not a good assumption). + bool model_decreasing = (model == "decreasing"); + for (size_t current_peak = 0; current_peak != old_spectrum.size(); ++current_peak) { const double current_mz = old_spectrum[current_peak].getMZ(); @@ -113,7 +118,7 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, { // Possible improvement: include proper averagine model filtering. for now start at the second peak to test hypothesis // Note: this is a common approach used in several other search engines - if (old_spectrum[p].getIntensity() > old_spectrum[extensions.back()].getIntensity()) + if (model_decreasing && old_spectrum[p].getIntensity() > old_spectrum[extensions.back()].getIntensity()) { has_min_isopeaks = (i >= min_isopeaks); break; diff --git a/src/pyOpenMS/pxds/Deisotoper.pxd b/src/pyOpenMS/pxds/Deisotoper.pxd index 87980a11e0c..33ad9e40946 100644 --- a/src/pyOpenMS/pxds/Deisotoper.pxd +++ b/src/pyOpenMS/pxds/Deisotoper.pxd @@ -9,9 +9,11 @@ cdef extern from "" namespace "Open # COMMENT: wrap static methods cdef extern from "" namespace "OpenMS::Deisotoper": + void deisotopeAndSingleCharge(MSSpectrum & spectra, double fragment_tolerance, bool fragment_unit_ppm, + String model, int min_charge, int max_charge, bool keep_only_deisotoped, @@ -20,3 +22,7 @@ cdef extern from "" namespace "Open bool make_single_charged, bool annotate_charge) nogil except + # wrap-attach:Deisotoper + void deisotopeAndSingleCharge(MSSpectrum & spectra, + double fragment_tolerance, + bool fragment_unit_ppm) nogil except + # wrap-attach:Deisotoper wrap-as:deisotopeAndSingleChargeDefault + From 669399b068667369c31ed5301d2f92b525d3b2ac Mon Sep 17 00:00:00 2001 From: Hannes Roest Date: Wed, 29 May 2019 09:12:03 -0400 Subject: [PATCH 050/471] [FIX] adapt code --- src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp | 1 + src/openms/source/ANALYSIS/OPENSWATH/SwathQC.cpp | 2 +- src/utils/AssayGeneratorMetabo.cpp | 1 + src/utils/RNPxlSearch.cpp | 1 + src/utils/SimpleSearchEngine.cpp | 1 - 5 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index e3dfd6c3956..c7fb1417afc 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -204,6 +204,7 @@ namespace OpenMS // deisotope Deisotoper::deisotopeAndSingleCharge(exp[exp_index], fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, + "decreasing", // model 1, 3, // min / max charge false, // keep only deisotoped 3, 10, // min / max isopeaks diff --git a/src/openms/source/ANALYSIS/OPENSWATH/SwathQC.cpp b/src/openms/source/ANALYSIS/OPENSWATH/SwathQC.cpp index b69ea4b30aa..4ebb3a7e85b 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/SwathQC.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/SwathQC.cpp @@ -112,7 +112,7 @@ namespace OpenSwath } // Note: this will pick up also non-peptide signals; filtering by averagine might yield better results - Deisotoper::deisotopeAndSingleCharge(tmp, this->decon_ms1_mz_tol_, false, 1, 10, true, 3, 10, false, true); + Deisotoper::deisotopeAndSingleCharge(tmp, this->decon_ms1_mz_tol_, false, "decreasing", 1, 10, true, 3, 10, false, true); if (tmp.getIntegerDataArrays().empty()) { throw Exception::Postcondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "IntegerDataArray must not be empty!"); diff --git a/src/utils/AssayGeneratorMetabo.cpp b/src/utils/AssayGeneratorMetabo.cpp index 1c95923eb95..9e07cd27384 100644 --- a/src/utils/AssayGeneratorMetabo.cpp +++ b/src/utils/AssayGeneratorMetabo.cpp @@ -494,6 +494,7 @@ class TOPPAssayGeneratorMetabo : Deisotoper::deisotopeAndSingleCharge(spectrum, fragment_tolerance, fragment_unit_ppm, + "decreasing", min_charge, max_charge, keep_only_deisotoped, diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/RNPxlSearch.cpp index e60297dab98..6ca0f2a9ba3 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/RNPxlSearch.cpp @@ -444,6 +444,7 @@ class RNPxlSearch : // deisotope Deisotoper::deisotopeAndSingleCharge(exp[exp_index], fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, + "decreasing", 1, 3, false, 2, 10, diff --git a/src/utils/SimpleSearchEngine.cpp b/src/utils/SimpleSearchEngine.cpp index ee70fe922f1..1732e802c17 100644 --- a/src/utils/SimpleSearchEngine.cpp +++ b/src/utils/SimpleSearchEngine.cpp @@ -49,7 +49,6 @@ #include // preprocessing and filtering -#include #include #include #include From 5f7dfc1a2528710d14a09b3fb9ed9c8d059bc215 Mon Sep 17 00:00:00 2001 From: Hannes Roest Date: Wed, 29 May 2019 09:13:12 -0400 Subject: [PATCH 051/471] [FEATURE] add tests --- .../openms/source/Deisotoper_test.cpp | 206 +++++++++++++----- 1 file changed, 150 insertions(+), 56 deletions(-) diff --git a/src/tests/class_tests/openms/source/Deisotoper_test.cpp b/src/tests/class_tests/openms/source/Deisotoper_test.cpp index 7131f78135e..e6abddff8cb 100644 --- a/src/tests/class_tests/openms/source/Deisotoper_test.cpp +++ b/src/tests/class_tests/openms/source/Deisotoper_test.cpp @@ -1,32 +1,32 @@ // -------------------------------------------------------------------------- -// OpenMS -- Open-Source Mass Spectrometry +// OpenMS -- Open-Source Mass Spectrometry // -------------------------------------------------------------------------- // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, // ETH Zurich, and Freie Universitaet Berlin 2002-2018. -// +// // This software is released under a three-clause BSD license: // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. -// * Neither the name of any author or any participating institution -// may be used to endorse or promote products derived from this software +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software // without specific prior written permission. -// For a full list of authors, refer to the file AUTHORS. +// For a full list of authors, refer to the file AUTHORS. // -------------------------------------------------------------------------- // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING -// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// +// // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Andreas Bertsch $ @@ -36,16 +36,18 @@ #include /////////////////////////// - -#include +#include #include #include #include #include -#include - +#include /////////////////////////// +#include +#include +#include + START_TEST(Deisotoper, "$Id$") ///////////////////////////////////////////////////////////// @@ -54,14 +56,15 @@ START_TEST(Deisotoper, "$Id$") using namespace OpenMS; using namespace std; - + START_SECTION(static void deisotopeAndSingleChargeMSSpectrum(MSSpectrum& in, - double fragment_tolerance, + double fragment_tolerance, bool fragment_unit_ppm, - int min_charge = 1, + std::string model = "none", + int min_charge = 1, int max_charge = 3, bool keep_only_deisotoped = false, - unsigned int min_isopeaks = 3, + unsigned int min_isopeaks = 3, unsigned int max_isopeaks = 10, bool make_single_charged = true, bool annotate_charge = false)) @@ -88,39 +91,41 @@ START_SECTION(static void deisotopeAndSingleChargeMSSpectrum(MSSpectrum& in, two_patterns.push_back(p); MSSpectrum theo0 = two_patterns; - Deisotoper::deisotopeAndSingleCharge(theo0, - 10.0, - true, - 1, - 2, - true, - 2, - 10, - false, - true); + Deisotoper::deisotopeAndSingleCharge(theo0, + 10.0, + true, + "decreasing", + 1, + 2, + true, + 2, + 10, + false, + true); TEST_EQUAL(theo0.size(), 2); // two peaks after deisotoping - TEST_REAL_SIMILAR(theo0[0].getMZ(), 100); - TEST_REAL_SIMILAR(theo0[1].getMZ(), 200); + TEST_REAL_SIMILAR(theo0[0].getMZ(), 100); + TEST_REAL_SIMILAR(theo0[1].getMZ(), 200); theo0 = two_patterns; - Deisotoper::deisotopeAndSingleCharge(theo0, - 10.0, - true, - 1, - 2, - true, - 2, - 10, - true, // convert to charge 1 - true); + Deisotoper::deisotopeAndSingleCharge(theo0, + 10.0, + true, + "decreasing", + 1, + 2, + true, + 2, + 10, + true, // convert to charge 1 + true); TEST_EQUAL(theo0.size(), 2); // two peaks after deisotoping - TEST_REAL_SIMILAR(theo0[0].getMZ(), 100); - TEST_REAL_SIMILAR(theo0[1].getMZ(), 400.0 - Constants::PROTON_MASS_U); + TEST_REAL_SIMILAR(theo0[0].getMZ(), 100); + TEST_REAL_SIMILAR(theo0[1].getMZ(), 400.0 - Constants::PROTON_MASS_U); - // create a theoretical spectrum generator + // create a theoretical spectrum generator // and configure to add isotope patterns TheoreticalSpectrumGenerator spec_generator; Param param = spec_generator.getParameters(); @@ -136,22 +141,111 @@ START_SECTION(static void deisotopeAndSingleChargeMSSpectrum(MSSpectrum& in, spec_generator.getSpectrum(theo1, peptide1, 1, 2); // charge 1..2 TEST_EQUAL(theo1.size(), 36); theo1.sortByPosition(); - Deisotoper::deisotopeAndSingleCharge(theo1, - 10.0, - true, - 1, - 2, - true, - 2, - 10, - false, - true); + Deisotoper::deisotopeAndSingleCharge(theo1, + 10.0, + true, + "decreasing", + 1, + 2, + true, + 2, + 10, + false, + true); // create theoretical spectrum without isotopic peaks for comparison to the deisotoped one param.setValue("add_isotopes", "false"); // disable additional isotopes spec_generator.setParameters(param); MSSpectrum theo1_noiso; spec_generator.getSpectrum(theo1_noiso, peptide1, 1, 2); // charge 1..2 TEST_EQUAL(theo1.size(), theo1_noiso.size()); // same number of peaks after deisotoping + + // test peptide DFPIANGER (mono-isotopic peak is highest) + { + int z = 5; + auto seq = AASequence::fromString("DFPIANGER"); + auto seq_formula = seq.getFormula() + EmpiricalFormula("H" + String(z)); + auto isotopes = seq_formula.getIsotopeDistribution( CoarseIsotopePatternGenerator(5) ); + + MSSpectrum s; + for (auto iso : isotopes.getContainer() ) + { + iso.setMZ( iso.getMZ() / z ); + s.push_back(iso); + } + Deisotoper::deisotopeAndSingleCharge(s, + 10.0, true, + "decreasing", + 1, z, + true, + 2, 10, + true, + true); + TEST_EQUAL(s.size(), 1); + // expect a single peak at the location of the [M+H]+ ion + TEST_REAL_SIMILAR(s[0].getMZ(), seq.getMonoWeight(Residue::ResidueType::Full, 1)); + TEST_REAL_SIMILAR(s[0].getMZ(), 1018.49798342972); + // test charge estimation + TEST_EQUAL(s.getIntegerDataArrays()[0][0], z); + } + + // test peptide DFPIANGERDFPIANGERDFPIANGERDFPIANGER (mono-isotopic peak is not the highest) + { + int z = 5; + auto seq = AASequence::fromString("DFPIANGERDFPIANGERDFPIANGERDFPIANGER"); + auto seq_formula = seq.getFormula() + EmpiricalFormula("H" + String(z)); + auto isotopes = seq_formula.getIsotopeDistribution( CoarseIsotopePatternGenerator(8) ); + + MSSpectrum s; + for (auto iso : isotopes.getContainer() ) // copy data + { + iso.setMZ( iso.getMZ() / z ); + s.push_back(iso); + } + Deisotoper::deisotopeAndSingleCharge(s, + 10.0, true, + "none", + 1, z, + true, + 2, 10, + true, + true); + // expect a single peak at the location of the [M+H]+ ion + TEST_EQUAL(s.size(), 1); + TEST_REAL_SIMILAR(s[0].getMZ(), seq.getMonoWeight(Residue::ResidueType::Full, 1)); + // test charge estimation + TEST_EQUAL(s.getIntegerDataArrays()[0][0], z); + } + + // test peptide DFPIANGERDFPIANGERDFPIANGERDFPIANGER (mono-isotopic peak is not the highest) with wrong settings + { + int z = 5; + auto seq = AASequence::fromString("DFPIANGERDFPIANGERDFPIANGERDFPIANGER"); + auto seq_formula = seq.getFormula() + EmpiricalFormula("H" + String(z)); + IsotopeDistribution isotopes = seq_formula.getIsotopeDistribution( CoarseIsotopePatternGenerator(8) ); + + MSSpectrum s; + for (auto iso : isotopes.getContainer() ) + { + iso.setMZ( iso.getMZ() / z ); + s.push_back(iso); + } + Deisotoper::deisotopeAndSingleCharge(s, + 10.0, true, + "decreasing", // WRONG - wont work + 1, z, + true, + 2, 10, + true, + true); + + // WRONG: model creates 3 peaks instead of a single peak + TEST_EQUAL(s.size(), 3); + TEST_REAL_SIMILAR(s[0].getMZ(), isotopes.getContainer()[0].getMZ()/z ); // wrong peak / left in place + TEST_REAL_SIMILAR(s[1].getMZ(), isotopes.getContainer()[1].getMZ()/z ); // wrong peak / left in place + TEST_REAL_SIMILAR(s[2].getMZ(), seq.getMonoWeight(Residue::ResidueType::Full, 3)); // 3rd isotope! + // test charge estimation + TEST_EQUAL(s.getIntegerDataArrays()[0][2], z); + } } END_SECTION From 0cb60ac606fbe77d20a80d4fbc18305971d7ab62 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Sat, 1 Jun 2019 14:47:25 +0200 Subject: [PATCH 052/471] Initial commit of NuXL --- doc/OpenMS_tutorial/OpenMS_Tutorial.doxygen | 2 +- doc/doxygen/public/UTILS.doxygen | 2 +- .../RNPXL/RNPxlModificationsGenerator.h | 2 +- .../RNPXL/RNPxlModificationsGenerator.cpp | 2 +- .../ANALYSIS/RNPXL/RNPxlParameterParsing.cpp | 2 +- .../source/APPLICATIONS/ToolHandler.cpp | 2 +- .../pxds/RNPxlModificationsGenerator.pxd | 2 +- .../RNPxlModificationsGenerator_test.cpp | 2 +- src/tests/topp/CMakeLists.txt | 60 ++++++------- src/tests/topp/IDFileConverter_20_input.idXML | 4 +- .../topp/IDFileConverter_20_output.pepXML | 6 +- ...h_1_input.fasta => OpenNuXL_1_input.fasta} | 0 ...rch_1_input.mzML => OpenNuXL_1_input.mzML} | 0 ...1_output.idXML => OpenNuXL_1_output.idXML} | 4 +- ...rameters.ini => OpenNuXL_1_parameters.ini} | 4 +- ...2_output.idXML => OpenNuXL_2_output.idXML} | 4 +- ...3_output.idXML => OpenNuXL_3_output.idXML} | 4 +- ...4_output.idXML => OpenNuXL_4_output.idXML} | 4 +- ...h_4_output2.tsv => OpenNuXL_4_output2.tsv} | 0 ...5_output.idXML => OpenNuXL_5_output.idXML} | 4 +- src/tests/topp/TextExporter_9_input.idXML | 2 +- src/tests/topp/TextExporter_9_output.csv | 14 ++-- src/tests/topp/TextExporter_9_output.txt | 14 ++-- src/topp/PercolatorAdapter.cpp | 2 +- src/utils/{RNPxlSearch.cpp => OpenNuXL.cpp} | 84 +++++++++---------- src/utils/executables.cmake | 2 +- tools/PythonExtensionChecker.py | 2 +- 27 files changed, 115 insertions(+), 115 deletions(-) rename src/tests/topp/{RNPxlSearch_1_input.fasta => OpenNuXL_1_input.fasta} (100%) rename src/tests/topp/{RNPxlSearch_1_input.mzML => OpenNuXL_1_input.mzML} (100%) rename src/tests/topp/{RNPxlSearch_1_output.idXML => OpenNuXL_1_output.idXML} (99%) rename src/tests/topp/{RNPxlSearch_1_parameters.ini => OpenNuXL_1_parameters.ini} (99%) rename src/tests/topp/{RNPxlSearch_2_output.idXML => OpenNuXL_2_output.idXML} (99%) rename src/tests/topp/{RNPxlSearch_3_output.idXML => OpenNuXL_3_output.idXML} (99%) rename src/tests/topp/{RNPxlSearch_4_output.idXML => OpenNuXL_4_output.idXML} (99%) rename src/tests/topp/{RNPxlSearch_4_output2.tsv => OpenNuXL_4_output2.tsv} (100%) rename src/tests/topp/{RNPxlSearch_5_output.idXML => OpenNuXL_5_output.idXML} (99%) rename src/utils/{RNPxlSearch.cpp => OpenNuXL.cpp} (98%) diff --git a/doc/OpenMS_tutorial/OpenMS_Tutorial.doxygen b/doc/OpenMS_tutorial/OpenMS_Tutorial.doxygen index ef1785934f7..78ecfa84e9c 100755 --- a/doc/OpenMS_tutorial/OpenMS_Tutorial.doxygen +++ b/doc/OpenMS_tutorial/OpenMS_Tutorial.doxygen @@ -187,7 +187,7 @@ The extensible %OpenMS library implements common mass spectrometric data process - Identification: - Database search: - Peptides (Tool %SimpleSearchEngine and its classes - started simple but is, by now, rather complete peptide identification engine) - - Protein-RNA cross-links (Tool %RNPxlSearch and its classes) + - Protein-NA cross-links (Tool %OpenNuXL and its classes) - Protein-Protein cross-links (Tool OpenPepXL) - Spectral library search: - Tool SpecLibSearcher and its classes diff --git a/doc/doxygen/public/UTILS.doxygen b/doc/doxygen/public/UTILS.doxygen index 77483a44fe1..5a2c6312507 100644 --- a/doc/doxygen/public/UTILS.doxygen +++ b/doc/doxygen/public/UTILS.doxygen @@ -86,7 +86,7 @@ Cross-linking - @subpage UTILS_OpenPepXL - Search for peptide pairs linked with a labeled cross-linker. - @subpage UTILS_OpenPepXLLF - Search for cross-linked peptide pairs in tandem MS spectra. - - @subpage UTILS_RNPxlSearch - Annotates RNA-to-peptide cross-links in MS/MS spectra. + - @subpage UTILS_OpenNuXL - Annotates NA-to-peptide cross-links in MS/MS spectra. - @subpage UTILS_RNPxlXICFilter - Removes MS2 spectra from treatment based on the fold change between control and treatment for RNA-to-peptide cross-linking experiments. - @subpage UTILS_XFDR - Calculates false discovery rate estimates on cross-link identifications. diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h index 333149a0f80..200a1714c79 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h @@ -56,7 +56,7 @@ namespace OpenMS class OPENMS_DLLAPI RNPxlModificationsGenerator { public: - static RNPxlModificationMassesResult initModificationMassesRNA(StringList target_nucleotides, + static RNPxlModificationMassesResult initModificationMassesNA(StringList target_nucleotides, StringList nt_groups, std::set can_xl, StringList mappings, diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp index 223b2c22944..47279376c21 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp @@ -65,7 +65,7 @@ bool RNPxlModificationsGenerator::notInSeq(String res_seq, String query) } //static -RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMassesRNA(StringList target_nucleotides, +RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMassesNA(StringList target_nucleotides, StringList nt_groups, std::set can_xl, StringList mappings, diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp index 80e299d8dcc..12f82daee82 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp @@ -211,7 +211,7 @@ RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringList fragment_ } } -#ifdef DEBUG_RNPXLSEARCH +#ifdef DEBUG_OpenNuXL for (auto const & p2fas : precursor_to_fragment_adducts) { for (auto const & p2fa : p2fas.second) diff --git a/src/openms/source/APPLICATIONS/ToolHandler.cpp b/src/openms/source/APPLICATIONS/ToolHandler.cpp index 0108bb08d92..29bb3298a85 100644 --- a/src/openms/source/APPLICATIONS/ToolHandler.cpp +++ b/src/openms/source/APPLICATIONS/ToolHandler.cpp @@ -237,7 +237,7 @@ namespace OpenMS util_map["QCShrinker"] = Internal::ToolDescription("QCExporter", util_category); util_map["RNADigestor"] = Internal::ToolDescription("RNADigestor", util_category); util_map["RNAMassCalculator"] = Internal::ToolDescription("RNAMassCalculator", util_category); - util_map["RNPxlSearch"] = Internal::ToolDescription("RNPxlSearch", util_category); + util_map["OpenNuXL"] = Internal::ToolDescription("OpenNuXL", util_category); util_map["RNPxlXICFilter"] = Internal::ToolDescription("RNPxlXICFilter", util_category); util_map["RTEvaluation"] = Internal::ToolDescription("RTEvaluation", util_category); util_map["SemanticValidator"] = Internal::ToolDescription("SemanticValidator", util_category); diff --git a/src/pyOpenMS/pxds/RNPxlModificationsGenerator.pxd b/src/pyOpenMS/pxds/RNPxlModificationsGenerator.pxd index 3238af2d011..f4fbe2942d9 100644 --- a/src/pyOpenMS/pxds/RNPxlModificationsGenerator.pxd +++ b/src/pyOpenMS/pxds/RNPxlModificationsGenerator.pxd @@ -15,7 +15,7 @@ cdef extern from "" namespa RNPxlModificationsGenerator() nogil except + RNPxlModificationsGenerator(RNPxlModificationsGenerator) nogil except + - RNPxlModificationMassesResult initModificationMassesRNA( + RNPxlModificationMassesResult initModificationMassesNA( StringList target_nucleotides, StringList nt_groups, libcpp_set[char] can_xl, diff --git a/src/tests/class_tests/openms/source/RNPxlModificationsGenerator_test.cpp b/src/tests/class_tests/openms/source/RNPxlModificationsGenerator_test.cpp index 3084a87dc41..e0fffb12b7f 100644 --- a/src/tests/class_tests/openms/source/RNPxlModificationsGenerator_test.cpp +++ b/src/tests/class_tests/openms/source/RNPxlModificationsGenerator_test.cpp @@ -61,7 +61,7 @@ START_SECTION(~RNPxlModificationsGenerator()) } END_SECTION -START_SECTION((static RNPxlModificationMassesResult initModificationMassesRNA(StringList target_nucleotides, StringList mappings, StringList restrictions, StringList modifications, String sequence_restriction, bool cysteine_adduct, Int max_length=4))) +START_SECTION((static RNPxlModificationMassesResult initModificationMassesNA(StringList target_nucleotides, StringList mappings, StringList restrictions, StringList modifications, String sequence_restriction, bool cysteine_adduct, Int max_length=4))) { // TODO } diff --git a/src/tests/topp/CMakeLists.txt b/src/tests/topp/CMakeLists.txt index 4bed06f6c3b..b84b0ff53cf 100644 --- a/src/tests/topp/CMakeLists.txt +++ b/src/tests/topp/CMakeLists.txt @@ -1700,43 +1700,43 @@ if(WITH_GUI) endif() #------------------------------------------------------------------------------ -# RNPxlSearch -add_test("TOPP_RNPxlSearch_1" ${TOPP_BIN_PATH}/RNPxlSearch -test -in -${DATA_DIR_TOPP}/RNPxlSearch_1_input.mzML -database ${DATA_DIR_TOPP}/RNPxlSearch_1_input.fasta -out RNPxlSearch_1_output.tmp -ini ${DATA_DIR_TOPP}/RNPxlSearch_1_parameters.ini) -add_test("TOPP_RNPxlSearch_1_out1" ${DIFF} -whitelist "IdentificationRun date" -"db=" -in1 RNPxlSearch_1_output.tmp -in2 ${DATA_DIR_TOPP}/RNPxlSearch_1_output.idXML ) -set_tests_properties("TOPP_RNPxlSearch_1_out1" PROPERTIES DEPENDS "TOPP_RNPxlSearch_1") +# OpenNuXL +add_test("TOPP_OpenNuXL_1" ${TOPP_BIN_PATH}/OpenNuXL -test -in +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_1_output.tmp -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini) +add_test("TOPP_OpenNuXL_1_out1" ${DIFF} -whitelist "IdentificationRun date" +"db=" -in1 OpenNuXL_1_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_1_output.idXML ) +set_tests_properties("TOPP_OpenNuXL_1_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_1") # test internal decoy generation -add_test("TOPP_RNPxlSearch_2" ${TOPP_BIN_PATH}/RNPxlSearch -test -in -${DATA_DIR_TOPP}/RNPxlSearch_1_input.mzML -database ${DATA_DIR_TOPP}/RNPxlSearch_1_input.fasta -out RNPxlSearch_2_output.tmp -RNPxl:decoys -ini ${DATA_DIR_TOPP}/RNPxlSearch_1_parameters.ini) -add_test("TOPP_RNPxlSearch_2_out1" ${DIFF} -whitelist "IdentificationRun date" -"db=" -in1 RNPxlSearch_2_output.tmp -in2 ${DATA_DIR_TOPP}/RNPxlSearch_2_output.idXML ) -set_tests_properties("TOPP_RNPxlSearch_2_out1" PROPERTIES DEPENDS "TOPP_RNPxlSearch_2") +add_test("TOPP_OpenNuXL_2" ${TOPP_BIN_PATH}/OpenNuXL -test -in +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_2_output.tmp -RNPxl:decoys -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini) +add_test("TOPP_OpenNuXL_2_out1" ${DIFF} -whitelist "IdentificationRun date" +"db=" -in1 OpenNuXL_2_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_2_output.idXML ) +set_tests_properties("TOPP_OpenNuXL_2_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_2") # reporting of multiple hits and tsv output -add_test("TOPP_RNPxlSearch_3" ${TOPP_BIN_PATH}/RNPxlSearch -test -in -${DATA_DIR_TOPP}/RNPxlSearch_1_input.mzML -database ${DATA_DIR_TOPP}/RNPxlSearch_1_input.fasta -out RNPxlSearch_3_output.tmp -report:top_hits 3 -out_tsv RNPxlSearch_3_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast) -add_test("TOPP_RNPxlSearch_3_out1" ${DIFF} -whitelist "IdentificationRun date" -"db=" -in1 RNPxlSearch_3_output.tmp -in2 ${DATA_DIR_TOPP}/RNPxlSearch_3_output.idXML ) -add_test("TOPP_RNPxlSearch_3_out2" ${DIFF} -in1 RNPxlSearch_3_output2.tmp -in2 ${DATA_DIR_TOPP}/RNPxlSearch_3_output2.tsv ) -set_tests_properties("TOPP_RNPxlSearch_3_out1" PROPERTIES DEPENDS "TOPP_RNPxlSearch_3") -set_tests_properties("TOPP_RNPxlSearch_3_out2" PROPERTIES DEPENDS "TOPP_RNPxlSearch_3") +add_test("TOPP_OpenNuXL_3" ${TOPP_BIN_PATH}/OpenNuXL -test -in +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_3_output.tmp -report:top_hits 3 -out_tsv OpenNuXL_3_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast) +add_test("TOPP_OpenNuXL_3_out1" ${DIFF} -whitelist "IdentificationRun date" +"db=" -in1 OpenNuXL_3_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_3_output.idXML ) +add_test("TOPP_OpenNuXL_3_out2" ${DIFF} -in1 OpenNuXL_3_output2.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_3_output2.tsv ) +set_tests_properties("TOPP_OpenNuXL_3_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_3") +set_tests_properties("TOPP_OpenNuXL_3_out2" PROPERTIES DEPENDS "TOPP_OpenNuXL_3") # reporting of multiple hits and tsv output and decoy generation -add_test("TOPP_RNPxlSearch_4" ${TOPP_BIN_PATH}/RNPxlSearch -test -in -${DATA_DIR_TOPP}/RNPxlSearch_1_input.mzML -RNPxl:decoys -database ${DATA_DIR_TOPP}/RNPxlSearch_1_input.fasta -out RNPxlSearch_4_output.tmp -report:top_hits 2 -out_tsv RNPxlSearch_4_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast) -add_test("TOPP_RNPxlSearch_4_out1" ${DIFF} -whitelist "IdentificationRun date" -"db=" -in1 RNPxlSearch_4_output.tmp -in2 ${DATA_DIR_TOPP}/RNPxlSearch_4_output.idXML ) -add_test("TOPP_RNPxlSearch_4_out2" ${DIFF} -in1 RNPxlSearch_4_output2.tmp -in2 ${DATA_DIR_TOPP}/RNPxlSearch_4_output2.tsv ) -set_tests_properties("TOPP_RNPxlSearch_4_out1" PROPERTIES DEPENDS "TOPP_RNPxlSearch_4") -set_tests_properties("TOPP_RNPxlSearch_4_out2" PROPERTIES DEPENDS "TOPP_RNPxlSearch_4") +add_test("TOPP_OpenNuXL_4" ${TOPP_BIN_PATH}/OpenNuXL -test -in +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -RNPxl:decoys -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_4_output.tmp -report:top_hits 2 -out_tsv OpenNuXL_4_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast) +add_test("TOPP_OpenNuXL_4_out1" ${DIFF} -whitelist "IdentificationRun date" +"db=" -in1 OpenNuXL_4_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_4_output.idXML ) +add_test("TOPP_OpenNuXL_4_out2" ${DIFF} -in1 OpenNuXL_4_output2.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_4_output2.tsv ) +set_tests_properties("TOPP_OpenNuXL_4_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_4") +set_tests_properties("TOPP_OpenNuXL_4_out2" PROPERTIES DEPENDS "TOPP_OpenNuXL_4") # test internal decoy generation - slow scoring -add_test("TOPP_RNPxlSearch_5" ${TOPP_BIN_PATH}/RNPxlSearch -test -in -${DATA_DIR_TOPP}/RNPxlSearch_1_input.mzML -database ${DATA_DIR_TOPP}/RNPxlSearch_1_input.fasta -out RNPxlSearch_5_output.tmp -RNPxl:decoys -ini ${DATA_DIR_TOPP}/RNPxlSearch_1_parameters.ini -RNPxl:scoring slow) -add_test("TOPP_RNPxlSearch_5_out1" ${DIFF} -whitelist "IdentificationRun date" -"db=" -in1 RNPxlSearch_5_output.tmp -in2 ${DATA_DIR_TOPP}/RNPxlSearch_5_output.idXML ) -set_tests_properties("TOPP_RNPxlSearch_5_out1" PROPERTIES DEPENDS "TOPP_RNPxlSearch_5") +add_test("TOPP_OpenNuXL_5" ${TOPP_BIN_PATH}/OpenNuXL -test -in +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_5_output.tmp -RNPxl:decoys -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini -RNPxl:scoring slow) +add_test("TOPP_OpenNuXL_5_out1" ${DIFF} -whitelist "IdentificationRun date" +"db=" -in1 OpenNuXL_5_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_5_output.idXML ) +set_tests_properties("TOPP_OpenNuXL_5_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_5") #------------------------------------------------------------------------------ # RTModel tests add_test("TOPP_RTModel_1" ${TOPP_BIN_PATH}/RTModel -test -in ${DATA_DIR_TOPP}/RTModel_1_input.idXML -out RTModel_1_output.tmp -ini ${DATA_DIR_TOPP}/RTModel_1_parameters.ini) diff --git a/src/tests/topp/IDFileConverter_20_input.idXML b/src/tests/topp/IDFileConverter_20_input.idXML index cd307c3009f..b262087d769 100644 --- a/src/tests/topp/IDFileConverter_20_input.idXML +++ b/src/tests/topp/IDFileConverter_20_input.idXML @@ -1,9 +1,9 @@ - + - + diff --git a/src/tests/topp/IDFileConverter_20_output.pepXML b/src/tests/topp/IDFileConverter_20_output.pepXML index 615f8a53641..a2690e3ea1a 100644 --- a/src/tests/topp/IDFileConverter_20_output.pepXML +++ b/src/tests/topp/IDFileConverter_20_output.pepXML @@ -1,11 +1,11 @@ - + - - + + diff --git a/src/tests/topp/RNPxlSearch_1_input.fasta b/src/tests/topp/OpenNuXL_1_input.fasta similarity index 100% rename from src/tests/topp/RNPxlSearch_1_input.fasta rename to src/tests/topp/OpenNuXL_1_input.fasta diff --git a/src/tests/topp/RNPxlSearch_1_input.mzML b/src/tests/topp/OpenNuXL_1_input.mzML similarity index 100% rename from src/tests/topp/RNPxlSearch_1_input.mzML rename to src/tests/topp/OpenNuXL_1_input.mzML diff --git a/src/tests/topp/RNPxlSearch_1_output.idXML b/src/tests/topp/OpenNuXL_1_output.idXML similarity index 99% rename from src/tests/topp/RNPxlSearch_1_output.idXML rename to src/tests/topp/OpenNuXL_1_output.idXML index 2416eade67a..20cea6c869f 100644 --- a/src/tests/topp/RNPxlSearch_1_output.idXML +++ b/src/tests/topp/OpenNuXL_1_output.idXML @@ -1,12 +1,12 @@ - + - + diff --git a/src/tests/topp/RNPxlSearch_1_parameters.ini b/src/tests/topp/OpenNuXL_1_parameters.ini similarity index 99% rename from src/tests/topp/RNPxlSearch_1_parameters.ini rename to src/tests/topp/OpenNuXL_1_parameters.ini index e4459d79840..f0ba4ca495b 100644 --- a/src/tests/topp/RNPxlSearch_1_parameters.ini +++ b/src/tests/topp/OpenNuXL_1_parameters.ini @@ -1,8 +1,8 @@ - + - + diff --git a/src/tests/topp/RNPxlSearch_2_output.idXML b/src/tests/topp/OpenNuXL_2_output.idXML similarity index 99% rename from src/tests/topp/RNPxlSearch_2_output.idXML rename to src/tests/topp/OpenNuXL_2_output.idXML index 3a6883ba925..87a4e71bb1a 100644 --- a/src/tests/topp/RNPxlSearch_2_output.idXML +++ b/src/tests/topp/OpenNuXL_2_output.idXML @@ -1,12 +1,12 @@ - + - + diff --git a/src/tests/topp/RNPxlSearch_3_output.idXML b/src/tests/topp/OpenNuXL_3_output.idXML similarity index 99% rename from src/tests/topp/RNPxlSearch_3_output.idXML rename to src/tests/topp/OpenNuXL_3_output.idXML index 4da50343b41..0acd3f97cdc 100644 --- a/src/tests/topp/RNPxlSearch_3_output.idXML +++ b/src/tests/topp/OpenNuXL_3_output.idXML @@ -1,12 +1,12 @@ - + - + diff --git a/src/tests/topp/RNPxlSearch_4_output.idXML b/src/tests/topp/OpenNuXL_4_output.idXML similarity index 99% rename from src/tests/topp/RNPxlSearch_4_output.idXML rename to src/tests/topp/OpenNuXL_4_output.idXML index 2901065f7af..0d6932a4297 100644 --- a/src/tests/topp/RNPxlSearch_4_output.idXML +++ b/src/tests/topp/OpenNuXL_4_output.idXML @@ -1,12 +1,12 @@ - + - + diff --git a/src/tests/topp/RNPxlSearch_4_output2.tsv b/src/tests/topp/OpenNuXL_4_output2.tsv similarity index 100% rename from src/tests/topp/RNPxlSearch_4_output2.tsv rename to src/tests/topp/OpenNuXL_4_output2.tsv diff --git a/src/tests/topp/RNPxlSearch_5_output.idXML b/src/tests/topp/OpenNuXL_5_output.idXML similarity index 99% rename from src/tests/topp/RNPxlSearch_5_output.idXML rename to src/tests/topp/OpenNuXL_5_output.idXML index dfb4b0ef385..e1049357e0f 100644 --- a/src/tests/topp/RNPxlSearch_5_output.idXML +++ b/src/tests/topp/OpenNuXL_5_output.idXML @@ -1,12 +1,12 @@ - + - + diff --git a/src/tests/topp/TextExporter_9_input.idXML b/src/tests/topp/TextExporter_9_input.idXML index 7bd87713192..92370492a80 100644 --- a/src/tests/topp/TextExporter_9_input.idXML +++ b/src/tests/topp/TextExporter_9_input.idXML @@ -3,7 +3,7 @@ - + diff --git a/src/tests/topp/TextExporter_9_output.csv b/src/tests/topp/TextExporter_9_output.csv index dfaaef58991..f2dfa60a63c 100644 --- a/src/tests/topp/TextExporter_9_output.csv +++ b/src/tests/topp/TextExporter_9_output.csv @@ -1,15 +1,15 @@ #RUN run_id score_type score_direction date_time search_engine_version parameters #PROTEIN score rank accession protein_description coverage sequence #PEPTIDE rt mz score rank sequence charge aa_before aa_after score_type search_identifier accessions predicted_rt predicted_pt scan_index A_136.06231 A_330.06033 C_112.05108 C_306.0491 G_152.05723 G_346.05525 RNPxl:Da difference RNPxl:RNA RNPxl:RNA_MASS_z0 RNPxl:best_localization RNPxl:best_localization_score RNPxl:peptide_mass_z0 RNPxl:ppm difference RNPxl:xl_mass_z0 RNPxl:z1 mass RNPxl:z2 mass RNPxl:z3 mass RNPxl:z4 mass U_113.03509 U_307.03311 protein_references target_decoy -RUN RNPxlSearch_2015-09-07T16:15:38 higher-score-better 2015-09-07T16:15:38 2.0.0 db=rnpxl_cas_1.fasta, db_version=, taxonomy=, charges=2:5, mass_type=monoisotopic, fixed_modifications=, variable_modifications=, enzyme=Unknown, missed_cleavages=1, peak_mass_tolerance=20, precursor_mass_tolerance=20 +RUN OpenNuXL_2015-09-07T16:15:38 higher-score-better 2015-09-07T16:15:38 2.0.0 db=rnpxl_cas_1.fasta, db_version=, taxonomy=, charges=2:5, mass_type=monoisotopic, fixed_modifications=, variable_modifications=, enzyme=Unknown, missed_cleavages=1, peak_mass_tolerance=20, precursor_mass_tolerance=20 PROTEIN 0 0 Cse1 -1 PROTEIN 0 0 Cse2 -1 PROTEIN 0 0 Cas7 -1 PROTEIN 0 0 Cas5 -1 PROTEIN 0 0 Cas6e -1 -PEPTIDE 17.7875061035156 712.782836914063 2.33490416097798 0 AEADNLDDKK 2 K L hyperscore RNPxlSearch_2015-09-07T16:15:38 Cas7 -1 -1 0 4.78868037462234 0 2.99854949116707 0 0 0 -0.000338330592057901 U-H2O1 306.0253048409 AEADNLDDkK 1.87158872621755 1117.5251393925 -0.474661755486804 1423.5504442334 1424.55772070017 712.782498583471 475.524091211238 356.894887525121 0 0 unique target -PEPTIDE 18.3059501647949 590.766052246094 2.00579096477783 0 LDSKGNIK 2 R R hyperscore RNPxlSearch_2015-09-07T16:15:38 Cas6e -1 -1 1 23.8672107458115 0 8.43987464904785 0 0 0 -0.000130290222955409 U-H2O1 306.0253048409 LDSkGNIK 2.17606346362403 873.4919861373 -0.22054458138691 1179.5172909782 1180.52456744497 590.765921955871 394.179706792838 295.886599211321 0 0 unique target -PEPTIDE 26.2365341186523 678.284423828125 3.01672363684849 0 DYHTVLGAR 2 R E hyperscore RNPxlSearch_2015-09-07T16:15:38 Cas5 -1 -1 3 69.618159532547 15.7811895012856 11.5055873990059 0 3.87108437716961 0 0.000586707496154304 U 324.0358699047 DyHTVLGAR 0.88477588747628 1030.519598233 0.864986675278286 1354.5554681377 1355.56274460447 678.285010535621 452.525765846004 339.646143501196 0 0 unique target -PEPTIDE 26.4131374359131 791.859008789063 2.10516378468165 0 KSEQTTGISLGR 2 K A hyperscore RNPxlSearch_2015-09-07T16:15:38 Cse2 -1 -1 4 100 18.3581411838531 1.60713978111744 0 0 0 6.30815079603053e-05 U-H2O1 306.0253048409 KsEQTTGISLGR 0.149626377165656 1275.6782859667 0.079662543754523 1581.7035908076 1582.71086727437 791.859071870571 528.241806735971 396.433174168671 0 0 unique target -PEPTIDE 28.4869823455811 828.696105957031 3.12100769461214 0 VEDVHPISERPQYFSGDGK 3 R S hyperscore RNPxlSearch_2015-09-07T16:15:38 Cas6e -1 -1 5 51.1079072952271 11.7230296134949 1.86482723802328 0 0 0 -0.000753345426460328 U 324.0358699047 VEDVHPISERPQyFSGDGK 2.01849083954261 2159.0283585298 -0.909074033160903 2483.0642284345 2484.07150490127 1242.53939068402 828.695352611605 621.773333575396 0 0 unique target -PEPTIDE 28.67844581604 656.794921875 1.75247453675492 0 FDQKIIDK 2 R T hyperscore RNPxlSearch_2015-09-07T16:15:38 Cas7 -1 -1 6 100 19.7569414973259 27.786260843277 1.10274739563465 8.62349197268486 0 -0.000242291528934402 U-H2O1 306.0253048409 FDQkIIDK 0.680211805073278 1005.5495013925 -0.368899956814601 1311.5748062334 1312.58208270017 656.794679583471 438.198878544571 328.900978025121 0 0 unique target +PEPTIDE 17.7875061035156 712.782836914063 2.33490416097798 0 AEADNLDDKK 2 K L hyperscore OpenNuXL_2015-09-07T16:15:38 Cas7 -1 -1 0 4.78868037462234 0 2.99854949116707 0 0 0 -0.000338330592057901 U-H2O1 306.0253048409 AEADNLDDkK 1.87158872621755 1117.5251393925 -0.474661755486804 1423.5504442334 1424.55772070017 712.782498583471 475.524091211238 356.894887525121 0 0 unique target +PEPTIDE 18.3059501647949 590.766052246094 2.00579096477783 0 LDSKGNIK 2 R R hyperscore OpenNuXL_2015-09-07T16:15:38 Cas6e -1 -1 1 23.8672107458115 0 8.43987464904785 0 0 0 -0.000130290222955409 U-H2O1 306.0253048409 LDSkGNIK 2.17606346362403 873.4919861373 -0.22054458138691 1179.5172909782 1180.52456744497 590.765921955871 394.179706792838 295.886599211321 0 0 unique target +PEPTIDE 26.2365341186523 678.284423828125 3.01672363684849 0 DYHTVLGAR 2 R E hyperscore OpenNuXL_2015-09-07T16:15:38 Cas5 -1 -1 3 69.618159532547 15.7811895012856 11.5055873990059 0 3.87108437716961 0 0.000586707496154304 U 324.0358699047 DyHTVLGAR 0.88477588747628 1030.519598233 0.864986675278286 1354.5554681377 1355.56274460447 678.285010535621 452.525765846004 339.646143501196 0 0 unique target +PEPTIDE 26.4131374359131 791.859008789063 2.10516378468165 0 KSEQTTGISLGR 2 K A hyperscore OpenNuXL_2015-09-07T16:15:38 Cse2 -1 -1 4 100 18.3581411838531 1.60713978111744 0 0 0 6.30815079603053e-05 U-H2O1 306.0253048409 KsEQTTGISLGR 0.149626377165656 1275.6782859667 0.079662543754523 1581.7035908076 1582.71086727437 791.859071870571 528.241806735971 396.433174168671 0 0 unique target +PEPTIDE 28.4869823455811 828.696105957031 3.12100769461214 0 VEDVHPISERPQYFSGDGK 3 R S hyperscore OpenNuXL_2015-09-07T16:15:38 Cas6e -1 -1 5 51.1079072952271 11.7230296134949 1.86482723802328 0 0 0 -0.000753345426460328 U 324.0358699047 VEDVHPISERPQyFSGDGK 2.01849083954261 2159.0283585298 -0.909074033160903 2483.0642284345 2484.07150490127 1242.53939068402 828.695352611605 621.773333575396 0 0 unique target +PEPTIDE 28.67844581604 656.794921875 1.75247453675492 0 FDQKIIDK 2 R T hyperscore OpenNuXL_2015-09-07T16:15:38 Cas7 -1 -1 6 100 19.7569414973259 27.786260843277 1.10274739563465 8.62349197268486 0 -0.000242291528934402 U-H2O1 306.0253048409 FDQkIIDK 0.680211805073278 1005.5495013925 -0.368899956814601 1311.5748062334 1312.58208270017 656.794679583471 438.198878544571 328.900978025121 0 0 unique target diff --git a/src/tests/topp/TextExporter_9_output.txt b/src/tests/topp/TextExporter_9_output.txt index 58fa9d30ce9..154718ea3c2 100644 --- a/src/tests/topp/TextExporter_9_output.txt +++ b/src/tests/topp/TextExporter_9_output.txt @@ -1,15 +1,15 @@ #RUN run_id score_type score_direction date_time search_engine_version parameters #PROTEIN score rank accession protein_description coverage sequence #PEPTIDE rt mz score rank sequence charge aa_before aa_after score_type search_identifier accessions predicted_rt predicted_pt scan_index A_136.06231 A_330.06033 C_112.05108 C_306.0491 G_152.05723 G_346.05525 RNPxl:Da difference RNPxl:RNA RNPxl:RNA_MASS_z0 RNPxl:best_localization RNPxl:best_localization_score RNPxl:peptide_mass_z0 RNPxl:ppm difference RNPxl:xl_mass_z0 RNPxl:z1 mass RNPxl:z2 mass RNPxl:z3 mass RNPxl:z4 mass U_113.03509 U_307.03311 protein_references target_decoy -RUN RNPxlSearch_2015-09-07T16:15:38_5233264595117471314 higher-score-better 2015-09-07T16:15:38 2.0.0 db=rnpxl_cas_1.fasta, db_version=, taxonomy=, charges=2:5, mass_type=monoisotopic, fixed_modifications=, variable_modifications=, enzyme=unknown_enzyme, missed_cleavages=1, peak_mass_tolerance=20.0, precursor_mass_tolerance=20.0 +RUN OpenNuXL_2015-09-07T16:15:38_5233264595117471314 higher-score-better 2015-09-07T16:15:38 2.0.0 db=rnpxl_cas_1.fasta, db_version=, taxonomy=, charges=2:5, mass_type=monoisotopic, fixed_modifications=, variable_modifications=, enzyme=unknown_enzyme, missed_cleavages=1, peak_mass_tolerance=20.0, precursor_mass_tolerance=20.0 PROTEIN 0 0 Cse1 -1 PROTEIN 0 0 Cse2 -1 PROTEIN 0 0 Cas7 -1 PROTEIN 0 0 Cas5 -1 PROTEIN 0 0 Cas6e -1 -PEPTIDE 17.7875061035156 712.782836914063 2.33490416097798 0 AEADNLDDKK 2 K L hyperscore RNPxlSearch_2015-09-07T16:15:38_5233264595117471314 Cas7 -1 -1 0 4.78868037462234 0.0 2.99854949116707 0.0 0.0 0.0 -3.38330592057901e-04 U-H2O1 306.025304840899992 AEADNLDDkK 1.87158872621755 1117.525139392500023 -0.474661755486804 1423.550444233399958 1424.557720700169966 712.782498583471011 475.524091211237987 356.894887525121021 0.0 0.0 unique target -PEPTIDE 18.3059501647949 590.766052246094 2.00579096477783 0 LDSKGNIK 2 R R hyperscore RNPxlSearch_2015-09-07T16:15:38_5233264595117471314 Cas6e -1 -1 1 23.867210745811502 0.0 8.43987464904785 0.0 0.0 0.0 -1.30290222955409e-04 U-H2O1 306.025304840899992 LDSkGNIK 2.17606346362403 873.491986137300046 -0.22054458138691 1179.517290978199981 1180.524567444969989 590.765921955871022 394.179706792837976 295.886599211321027 0.0 0.0 unique target -PEPTIDE 26.2365341186523 678.284423828125 3.01672363684849 0 DYHTVLGAR 2 R E hyperscore RNPxlSearch_2015-09-07T16:15:38_5233264595117471314 Cas5 -1 -1 3 69.618159532546997 15.781189501285599 11.505587399005901 0.0 3.87108437716961 0.0 5.86707496154304e-04 U 324.035869904700007 DyHTVLGAR 0.88477588747628 1030.519598232999897 0.864986675278286 1354.555468137700018 1355.562744604470026 678.285010535621041 452.525765846003992 339.646143501195979 0.0 0.0 unique target -PEPTIDE 26.4131374359131 791.859008789063 2.10516378468165 0 KSEQTTGISLGR 2 K A hyperscore RNPxlSearch_2015-09-07T16:15:38_5233264595117471314 Cse2 -1 -1 4 100.0 18.3581411838531 1.60713978111744 0.0 0.0 0.0 6.30815079603053e-05 U-H2O1 306.025304840899992 KsEQTTGISLGR 0.149626377165656 1275.678285966700059 0.079662543754523 1581.703590807599994 1582.710867274370003 791.859071870571029 528.241806735970954 396.433174168670973 0.0 0.0 unique target -PEPTIDE 28.4869823455811 828.696105957031 3.12100769461214 0 VEDVHPISERPQYFSGDGK 3 R S hyperscore RNPxlSearch_2015-09-07T16:15:38_5233264595117471314 Cas6e -1 -1 5 51.107907295227101 11.7230296134949 1.86482723802328 0.0 0.0 0.0 -7.53345426460328e-04 U 324.035869904700007 VEDVHPISERPQyFSGDGK 2.01849083954261 2159.028358529799789 -0.909074033160903 2483.06422843449991 2484.071504901270146 1242.539390684019963 828.695352611605017 621.773333575396009 0.0 0.0 unique target -PEPTIDE 28.67844581604 656.794921875 1.75247453675492 0 FDQKIIDK 2 R T hyperscore RNPxlSearch_2015-09-07T16:15:38_5233264595117471314 Cas7 -1 -1 6 100.0 19.756941497325901 27.786260843276999 1.10274739563465 8.62349197268486 0.0 -2.42291528934402e-04 U-H2O1 306.025304840899992 FDQkIIDK 0.680211805073278 1005.549501392500019 -0.368899956814601 1311.574806233400068 1312.582082700170076 656.794679583470952 438.198878544571016 328.900978025120992 0.0 0.0 unique target +PEPTIDE 17.7875061035156 712.782836914063 2.33490416097798 0 AEADNLDDKK 2 K L hyperscore OpenNuXL_2015-09-07T16:15:38_5233264595117471314 Cas7 -1 -1 0 4.78868037462234 0.0 2.99854949116707 0.0 0.0 0.0 -3.38330592057901e-04 U-H2O1 306.025304840899992 AEADNLDDkK 1.87158872621755 1117.525139392500023 -0.474661755486804 1423.550444233399958 1424.557720700169966 712.782498583471011 475.524091211237987 356.894887525121021 0.0 0.0 unique target +PEPTIDE 18.3059501647949 590.766052246094 2.00579096477783 0 LDSKGNIK 2 R R hyperscore OpenNuXL_2015-09-07T16:15:38_5233264595117471314 Cas6e -1 -1 1 23.867210745811502 0.0 8.43987464904785 0.0 0.0 0.0 -1.30290222955409e-04 U-H2O1 306.025304840899992 LDSkGNIK 2.17606346362403 873.491986137300046 -0.22054458138691 1179.517290978199981 1180.524567444969989 590.765921955871022 394.179706792837976 295.886599211321027 0.0 0.0 unique target +PEPTIDE 26.2365341186523 678.284423828125 3.01672363684849 0 DYHTVLGAR 2 R E hyperscore OpenNuXL_2015-09-07T16:15:38_5233264595117471314 Cas5 -1 -1 3 69.618159532546997 15.781189501285599 11.505587399005901 0.0 3.87108437716961 0.0 5.86707496154304e-04 U 324.035869904700007 DyHTVLGAR 0.88477588747628 1030.519598232999897 0.864986675278286 1354.555468137700018 1355.562744604470026 678.285010535621041 452.525765846003992 339.646143501195979 0.0 0.0 unique target +PEPTIDE 26.4131374359131 791.859008789063 2.10516378468165 0 KSEQTTGISLGR 2 K A hyperscore OpenNuXL_2015-09-07T16:15:38_5233264595117471314 Cse2 -1 -1 4 100.0 18.3581411838531 1.60713978111744 0.0 0.0 0.0 6.30815079603053e-05 U-H2O1 306.025304840899992 KsEQTTGISLGR 0.149626377165656 1275.678285966700059 0.079662543754523 1581.703590807599994 1582.710867274370003 791.859071870571029 528.241806735970954 396.433174168670973 0.0 0.0 unique target +PEPTIDE 28.4869823455811 828.696105957031 3.12100769461214 0 VEDVHPISERPQYFSGDGK 3 R S hyperscore OpenNuXL_2015-09-07T16:15:38_5233264595117471314 Cas6e -1 -1 5 51.107907295227101 11.7230296134949 1.86482723802328 0.0 0.0 0.0 -7.53345426460328e-04 U 324.035869904700007 VEDVHPISERPQyFSGDGK 2.01849083954261 2159.028358529799789 -0.909074033160903 2483.06422843449991 2484.071504901270146 1242.539390684019963 828.695352611605017 621.773333575396009 0.0 0.0 unique target +PEPTIDE 28.67844581604 656.794921875 1.75247453675492 0 FDQKIIDK 2 R T hyperscore OpenNuXL_2015-09-07T16:15:38_5233264595117471314 Cas7 -1 -1 6 100.0 19.756941497325901 27.786260843276999 1.10274739563465 8.62349197268486 0.0 -2.42291528934402e-04 U-H2O1 306.025304840899992 FDQkIIDK 0.680211805073278 1005.549501392500019 -0.368899956814601 1311.574806233400068 1312.582082700170076 656.794679583470952 438.198878544571016 328.900978025120992 0.0 0.0 unique target diff --git a/src/topp/PercolatorAdapter.cpp b/src/topp/PercolatorAdapter.cpp index a2ea543433d..92d39786387 100644 --- a/src/topp/PercolatorAdapter.cpp +++ b/src/topp/PercolatorAdapter.cpp @@ -457,7 +457,7 @@ class PercolatorAdapter : float isoErr = hit.getMetaValue("IsotopeError").toString().toFloat(); exp_mass = exp_mass - (isoErr * Constants::C13C12_MASSDIFF_U) / charge; } - else if (hit.metaValueExists("isotope_error")) // e.g. SimpleSearchEngine /RNPxlSearch + else if (hit.metaValueExists("isotope_error")) // e.g. SimpleSearchEngine /OpenNuXL { float isoErr = hit.getMetaValue("isotope_error").toString().toFloat(); exp_mass = exp_mass - (isoErr * Constants::C13C12_MASSDIFF_U) / charge; diff --git a/src/utils/RNPxlSearch.cpp b/src/utils/OpenNuXL.cpp similarity index 98% rename from src/utils/RNPxlSearch.cpp rename to src/utils/OpenNuXL.cpp index 3192c1c4560..1cff8c0637d 100644 --- a/src/utils/RNPxlSearch.cpp +++ b/src/utils/OpenNuXL.cpp @@ -99,7 +99,7 @@ #define NUMBER_OF_THREADS (1) #endif -//#define DEBUG_RNPXLSEARCH 1 +//#define DEBUG_OpenNuXL 1 using namespace OpenMS; using namespace OpenMS::Internal; @@ -200,27 +200,27 @@ class AnnotatedHit //------------------------------------------------------------- /** - @page UTILS_RNPxlSearch RNPxlSearch + @page UTILS_OpenNuXL OpenNuXL - @brief Annotate RNA to peptide crosslinks in MS/MS spectra. + @brief Annotate NA to peptide crosslinks in MS/MS spectra. The command line parameters of this tool are: - @verbinclude UTILS_RNPxlSearch.cli + @verbinclude UTILS_OpenNuXL.cli INI file documentation of this tool: - @htmlinclude UTILS_RNPxlSearch.html + @htmlinclude UTILS_OpenNuXL.html */ // We do not want this class to show up in the docu: /// @cond TOPPCLASSES -class RNPxlSearch : +class OpenNuXL : public TOPPBase { bool fast_scoring_ = true; // fast or all fragment adduct scoring mode set can_xl_; ///< nucleotides that can form cross-links public: - RNPxlSearch() : - TOPPBase("RNPxlSearch", "Annotate RNA/DNA-peptide cross-links in MS/MS spectra.", false) + OpenNuXL() : + TOPPBase("OpenNuXL", "Annotate RNA/DNA-peptide cross-links in MS/MS spectra.", false) { } @@ -989,7 +989,7 @@ static void scoreShiftedFragments_( plss_modds, plss_pc_MIC, plss_im_MIC); -#ifdef DEBUG_RNPXLSEARCH +#ifdef DEBUG_OpenNuXL LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif // cap plss_err to something larger than the mean_mz * max_ppm_error @@ -1052,7 +1052,7 @@ static void scoreShiftedFragments_( DataArrays::IntegerDataArray& ia = spec.getIntegerDataArrays()[0]; // charge array for (int & z : ia) { if (z == 0) { z = 1; } } } - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL cout << "after deisotoping..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; cout << "Fragment charges in spectrum: " << exp_index << endl; @@ -1065,7 +1065,7 @@ static void scoreShiftedFragments_( // remove noise window_mower_filter.filterPeakSpectrum(spec); - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL cout << "after mower..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; for (Size i = 0; i != spec.size(); ++i) cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << endl; @@ -1077,7 +1077,7 @@ static void scoreShiftedFragments_( nlargest_filter.filterPeakSpectrum(spec); - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL cout << "after nlargest..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; for (Size i = 0; i != spec.size(); ++i) cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << endl; @@ -1090,7 +1090,7 @@ static void scoreShiftedFragments_( // sort (nlargest changes order) spec.sortByPosition(); - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL cout << "after sort..." << endl; cout << "Fragment m/z and intensities for spectrum: " << exp_index << endl; for (Size i = 0; i != spec.size(); ++i) cout << spec[i].getMZ() << "\t" << spec.getIntensity() << endl; @@ -1143,7 +1143,7 @@ static void scoreShiftedFragments_( assert(exp.size() == annotated_hits.size()); - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << exp.size() << " : " << annotated_hits.size() << endl; #endif @@ -1227,7 +1227,7 @@ static void scoreShiftedFragments_( if (precursor_rna_adduct == "none") { - ah.score = RNPxlSearch::calculateCombinedScore(ah, false); + ah.score = OpenNuXL::calculateCombinedScore(ah, false); continue; } @@ -1327,7 +1327,7 @@ static void scoreShiftedFragments_( ah.marker_ions_score = marker_ions_sub_score; ah.partial_loss_score = partial_loss_sub_score; // combined score - ah.score = RNPxlSearch::calculateCombinedScore(ah, true); + ah.score = OpenNuXL::calculateCombinedScore(ah, true); } } } @@ -1462,7 +1462,7 @@ static void scoreShiftedFragments_( annotated_immonium_ions; // first annotate total loss peaks (these give no information where the actual shift occured) - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "Annotating ion (total loss spectrum): " << fixed_and_variable_modified_peptide.toString() << endl; #endif vector> alignment; @@ -1518,7 +1518,7 @@ static void scoreShiftedFragments_( Size ion_number = (Size)ion_nr_string.toInt(); RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); unshifted_y_ions[ion_number].push_back(d); - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL const AASequence& peptide_sequence = fixed_and_variable_modified_peptide.getSuffix(ion_number); OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; #endif @@ -1545,7 +1545,7 @@ static void scoreShiftedFragments_( { String ion_nr_string = ion_name.substr(1, charge_pos - 1); Size ion_number = (Size)ion_nr_string.toInt(); - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL const AASequence& peptide_sequence = aas.getPrefix(ion_number); OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; #endif @@ -1574,7 +1574,7 @@ static void scoreShiftedFragments_( { String ion_nr_string = ion_name.substr(1, charge_pos - 1); auto ion_number = (Size)ion_nr_string.toInt(); - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL const AASequence& peptide_sequence = aas.getPrefix(ion_number); OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; #endif @@ -1668,14 +1668,14 @@ static void scoreShiftedFragments_( const double & fragment_intensity = fragment.getIntensity(); // in percent (%) const double & fragment_mz = fragment.getMZ(); const int & fragment_charge = exp_spectrum.getIntegerDataArrays().back()[fragment_index]; - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "fragment_mz:" << fragment_mz << " fragment_charge:" << fragment_charge << endl; #endif String ion_name = partial_loss_annotations[pair_it->first]; const int charge = partial_loss_charges[pair_it->first]; - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "theo_name:" << ion_name << " theo_charge:" << charge << endl; #endif vector f; @@ -1686,7 +1686,7 @@ static void scoreShiftedFragments_( String fragment_ion_name = f[0]; // e.g. y3 - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << " intensity: " << fragment_intensity << endl; #endif @@ -1803,7 +1803,7 @@ static void scoreShiftedFragments_( for (auto& k : unshifted_y_ions[ion_index]) { c_noshifts[i] += k.intensity; } } -#ifdef DEBUG_RNPXLSEARCH +#ifdef DEBUG_OpenNuXL cout << "n:"; for (auto& k : n_shifts) cout << k << " "; cout << endl; @@ -1848,13 +1848,13 @@ static void scoreShiftedFragments_( for (int j = i; j >= 0; --j) { sites_sum_score[i] += c_shifts[j]; } } } -#ifdef DEBUG_RNPXLSEARCH +#ifdef DEBUG_OpenNuXL cout << "site sum score (shifted a/b/y-ions):"; for (auto& k : sites_sum_score) cout << k << " "; cout << endl; #endif - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "Localisation based on immonium ions: "; #endif String aas_unmodified = aas.toUnmodifiedString(); @@ -1871,7 +1871,7 @@ static void scoreShiftedFragments_( } } } -#ifdef DEBUG_RNPXLSEARCH +#ifdef DEBUG_OpenNuXL cout << "site sum score (shifted a/b/y-ions & immonium ions):"; for (auto& k : sites_sum_score) cout << k << " "; cout << endl; @@ -1887,7 +1887,7 @@ static void scoreShiftedFragments_( for (Size i = 0; i != sites_sum_score.size(); ++i) { - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << String::number(100.0 * sites_sum_score[i], 2); #endif @@ -1906,7 +1906,7 @@ static void scoreShiftedFragments_( best_localization[i] = tolower(best_localization[i]); } } - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << endl; #endif @@ -1925,7 +1925,7 @@ static void scoreShiftedFragments_( a.best_localization_score = best_localization_score; a.fragment_annotations = fas; - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "Ion centric annotation: " << endl; OPENMS_LOG_DEBUG << "unshifted b ions: " << endl; OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("b", unshifted_b_ions) << endl; @@ -2073,9 +2073,9 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("RNPxl:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses - ph.setMetaValue(String("RNPxl:RNA"), *mod_combinations_it->second.begin()); // return first nucleotide formula matching the index of the empirical formula + ph.setMetaValue(String("RNPxl:NA"), *mod_combinations_it->second.begin()); // return first nucleotide formula matching the index of the empirical formula ph.setMetaValue(String("RNPxl:NT"), String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide - ph.setMetaValue(String("RNPxl:RNA_MASS_z0"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight()); // NA uncharged mass via empirical formula + ph.setMetaValue(String("RNPxl:NA_MASS_z0"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight()); // NA uncharged mass via empirical formula ph.setMetaValue(String("RNPxl:isXL"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight() > 0); ph.setMetaValue(String("RNPxl:isPhospho"), is_phospho); @@ -2117,7 +2117,7 @@ static void scoreShiftedFragments_( // protein identifications (leave as is...) protein_ids = vector(1); protein_ids[0].setDateTime(DateTime::now()); - protein_ids[0].setSearchEngine("RNPxlSearch"); + protein_ids[0].setSearchEngine("OpenNuXL"); protein_ids[0].setSearchEngineVersion(VersionInfo::getVersion()); ProteinIdentification::SearchParameters search_parameters; search_parameters.db = getStringOption_("database"); @@ -2159,7 +2159,7 @@ static void scoreShiftedFragments_( << "RNPxl:pl_pc_MIC" << "RNPxl:pl_im_MIC" << "RNPxl:total_MIC" - << "RNPxl:RNA_MASS_z0" + << "RNPxl:NA_MASS_z0" << "RNPxl:ladder_score" << "RNPxl:sequence_score" << "precursor_intensity_log10"; @@ -2328,7 +2328,7 @@ static void scoreShiftedFragments_( // simple combined score in fast scoring: ah.score = total_loss_score + ah.total_MIC + mass_error_score / 3.0; - #ifdef DEBUG_RNPXLSEARCH + #ifdef DEBUG_OpenNuXL LOG_DEBUG << "best score in pre-score: " << score << endl; #endif @@ -2526,7 +2526,7 @@ static void scoreShiftedFragments_( RNPxlModificationMassesResult mm; if (max_nucleotide_length != 0) { - mm = RNPxlModificationsGenerator::initModificationMassesRNA( + mm = RNPxlModificationsGenerator::initModificationMassesNA( target_nucleotides, nt_groups, can_xl_, @@ -2852,9 +2852,9 @@ static void scoreShiftedFragments_( } // combined score - ah.score = RNPxlSearch::calculateCombinedScore(ah, false); + ah.score = OpenNuXL::calculateCombinedScore(ah, false); -#ifdef DEBUG_RNPXLSEARCH +#ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; #endif @@ -3044,9 +3044,9 @@ static void scoreShiftedFragments_( } // combined score - ah.score = RNPxlSearch::calculateCombinedScore(ah, true); + ah.score = OpenNuXL::calculateCombinedScore(ah, true); -#ifdef DEBUG_RNPXLSEARCH +#ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; #endif @@ -3276,7 +3276,7 @@ static void scoreShiftedFragments_( plss_err = plss_Morph > 2 ? pl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; plss_modds = matchOddsScore_(pl_spec->size(), (int)plss_Morph); } -#ifdef DEBUG_RNPXLSEARCH +#ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif // cap plss_err to something larger than the mean_mz * max_ppm_error @@ -3287,7 +3287,7 @@ static void scoreShiftedFragments_( int main(int argc, const char** argv) { - RNPxlSearch tool; + OpenNuXL tool; return tool.main(argc, argv); } diff --git a/src/utils/executables.cmake b/src/utils/executables.cmake index caa2426179f..168565bee9f 100644 --- a/src/utils/executables.cmake +++ b/src/utils/executables.cmake @@ -53,7 +53,7 @@ QCShrinker RNADigestor RNAMassCalculator RNPxlXICFilter -RNPxlSearch +OpenNuXL RTEvaluation SemanticValidator SequenceCoverageCalculator diff --git a/tools/PythonExtensionChecker.py b/tools/PythonExtensionChecker.py index 199bb78ad3b..4e5913d3d05 100755 --- a/tools/PythonExtensionChecker.py +++ b/tools/PythonExtensionChecker.py @@ -1145,7 +1145,7 @@ def pxd_text_printout(pxd_text, pxds_out, comp_name, print_pxd): elif comp_name.startswith("KDTree::"): # KD Tree namespace continue - elif not (comp_name.startswith("OpenMS") or comp_name.startswith("OpenSwath") or comp_name.startswith("RNPxl") ): + elif not (comp_name.startswith("OpenMS") or comp_name.startswith("OpenSwath") or comp_name.startswith("OpenNuXL") ): # Continue without checking or generating a testreport print ("Unknown namespace", comp_name) continue From 90657b717d7a3cc9188fcf7ee3bd44389cd95e6b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 18 Jun 2019 17:17:47 +0200 Subject: [PATCH 053/471] [FIX,DOC] removed some old custom mods from unimod, added documentation --- share/OpenMS/CHEMISTRY/unimod.xml | 165 ------------------ .../source/ANALYSIS/RNPXL/RNPxlReport.cpp | 25 ++- .../source/VISUAL/Spectrum1DCanvas.cpp | 3 +- src/utils/OpenNuXL.cpp | 141 ++++++++++++--- 4 files changed, 131 insertions(+), 203 deletions(-) diff --git a/share/OpenMS/CHEMISTRY/unimod.xml b/share/OpenMS/CHEMISTRY/unimod.xml index 3ebf6958752..98f5cc54f04 100644 --- a/share/OpenMS/CHEMISTRY/unimod.xml +++ b/share/OpenMS/CHEMISTRY/unimod.xml @@ -37818,47 +37818,6 @@ antiserum and mass spectrometric analysis LRGG ubiquitin remnant with dimethylated Arg LRGG remnant of ubiquitin remaining attached to lysine with missed cleavage due to dimethylation of arginine - - - - - - - - - - - - Photo-cross-linking and high-resolution mass spectrometry for assignment of RNRNA-binding sites in RNRNA-binding proteins - Journal - https://doi.org/10.1038/nmeth.3092 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp index e6bdd36dd14..d67bfc7dcd0 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp @@ -163,12 +163,6 @@ namespace OpenMS // this ensures that sequences with additional reported partial loss match the total weight // Note that the partial loss is only relevent on the MS2 and would otherwise be added to the totalweight String sequence_string = ph.getSequence().toString(); - sequence_string.substitute("(RNA:U_prime-H2O)", ""); - sequence_string.substitute("(RNA:U_prime)", ""); - sequence_string.substitute("(RNA:U-H3PO4)", ""); - sequence_string.substitute("(RNA:U-H2O)", ""); - sequence_string.substitute("(RNA:U)", ""); - sequence_string.substitute("(RNA:C3O)", ""); const AASequence sequence = AASequence::fromString(sequence_string); @@ -255,29 +249,32 @@ namespace OpenMS // If already modified search for an unmodified amino acid and add it there if (rna_weight > 0) { - const AASequence& aa = ph.getSequence(); + AASequence aa = ph.getSequence(); const String seq = ph.getSequence().toString(); if (!aa.hasCTerminalModification()) { - AASequence new_aa = AASequence::fromString(seq + ".[" + String(rna_weight) + "]"); - ph.setSequence(new_aa); + aa = AASequence::fromString(seq + ".[" + String(rna_weight) + "]"); + ph.setSequence(aa); } else if (!aa.hasNTerminalModification()) { - AASequence new_aa = AASequence::fromString("[" + String(rna_weight) + "]." + seq); - ph.setSequence(new_aa); + aa = AASequence::fromString("[" + String(rna_weight) + "]." + seq); + ph.setSequence(aa); } else // place it anywhere { - for (auto a : aa) // NOTE: performs copy, this cannot possibly work! + Size index(0); + for (auto & a : aa) { if (!a.isModified()) { - a.setModification("[" + String(rna_weight) + "]"); + aa.setModification(index, "[" + String(rna_weight) + "]"); break; } - } + ++index; + } + ph.setSequence(aa); } } } diff --git a/src/openms_gui/source/VISUAL/Spectrum1DCanvas.cpp b/src/openms_gui/source/VISUAL/Spectrum1DCanvas.cpp index dba9cf4bc68..cc4fabaa58c 100644 --- a/src/openms_gui/source/VISUAL/Spectrum1DCanvas.cpp +++ b/src/openms_gui/source/VISUAL/Spectrum1DCanvas.cpp @@ -1071,8 +1071,9 @@ namespace OpenMS // deisotope so we don't consider higher isotopic peaks Deisotoper::deisotopeAndSingleCharge(spec, - 100, // tolerance + 100, // tolerance true, // ppm + "none", // no isotope model 1, 6, // min / max charge false, // keep only deisotoped 3, 10, // min / max isopeaks diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 3b4847ad327..814e680fba0 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -124,6 +124,8 @@ struct ImmoniumIonsInPeptide case 'L': L = true; break; case 'K': K = true; break; case 'M': M = true; break; + case 'Q': Q = true; break; + case 'E': E = true; break; default: break; } } @@ -137,6 +139,8 @@ struct ImmoniumIonsInPeptide bool L = false; bool K = false; bool M = false; + bool Q = false; + bool E = false; }; /// Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space @@ -153,35 +157,95 @@ class AnnotatedHit static constexpr const char UNKNOWN_NUCLEOTIDE = '?'; char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE; - // main score + + /** + The main score (score) is a linear combination of (weighted) subscores + */ float score = 0; + // + // Scores exclusively calculated from peaks without nucleotide shifts: + // + + /** + The total loss score is the X!Tandem HyperScore calculated from b-,y-ions + without any nucleotide shift. + */ float total_loss_score = 0; - // total loss morpheus related subscores + + /** + The matched ion current in immonium (immonium_score) and precursor ions (precursor_score) + without any nucleotide shift. + */ + float immonium_score = 0; + float precursor_score = 0; + + /** + The matched ion current (MIC), average fragment error (err), and morpheus score (Morph) are calculated + for b-,y-,a-ions without nucleotide shift. Morph is just the number of matched peaks + the fraction of MIC + */ float MIC = 0; float err = 0; float Morph = 0; - float modds = 0; // match odds + /** + The match odds score (modds), uses a cumulativ binomial distribution to calculate the odds + of observing that many matched peaks by chance. + */ + float modds = 0; + + // + // Scores exclusively calculated from nucleotide shifted peaks: + // + + /** + The partial loss score is the X!Tandem HyperScore calculated from b-,y-ions + with nucleotide shifts. + */ + float partial_loss_score = 0; - // partial loss morpheus related subscores + /** + The matched ion current (pl_MIC), average fragment error (pl_err), and morpheus score (pl_Morph) are calculated + from b-,y-,a-ions with nucleotide shift. + Morph: number of matched peaks + the fraction of MIC + */ float pl_MIC = 0; float pl_err = 0; float pl_Morph = 0; - float pl_modds = 0; // match odds + float pl_modds = 0; float pl_pc_MIC = 0; float pl_im_MIC = 0; - // complete TIC fraction of explained peaks + // + // Scores calculated from peaks with AND without nucleotide shifts: + // + + /** + The complete TIC fraction of explained peaks (total_MIC) (excludes marker ions) + For peptides: total_MIC = MIC + im_MIC + pc_MIC (b-,a-,y-ions, immonium ions, precursor ions) + For XLs: total_MIC = MIC + im_MIC + pc_MIC + pl_MIC + pl_pc_MIC + pl_im_MIC (same as above + shifted versions) + */ float total_MIC = 0; - // subscores - float partial_loss_score = 0; - float immonium_score = 0; - float precursor_score = 0; + /** + The matched ion current in marker ions (marker_ions_score) is not considered in scoring. + */ float marker_ions_score = 0; + /** + Coverage of peptide by prefix or suffix ions (fraction) + For example: PEPTIDER + 01000100 (two of eight ions observed -> 2/8) + Shifted and non-shifted are combined to determine coverage. + */ float ladder_score = 0; + /** + Longest sequence covered in peptide by prefix or suffix ions (fraction). + Coverage of peptide by prefix or suffix ions (fraction) + For example: PEPTIDER + 01110001 (three ions form the longest sequence -> 3/8) + Shifted and non-shifted are combined to determine coverage. + */ float sequence_score = 0; float best_localization_score = 0; @@ -367,6 +431,8 @@ class OpenNuXL : { if (matched_size < 1 || N < 1) { return 0; } + // TODO: try p = Nd/w (number of peaks in spectrum * fragment mass tolerance in Da / MS/MS mass range in Da - see phoshoRS) + const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see ThresholdMower) const double pscore = boost::math::ibeta(matched_size + 1, N - matched_size, p); if (pscore <= std::numeric_limits::min()) return -log10(std::numeric_limits::min()); @@ -603,23 +669,20 @@ class OpenNuXL : } }; - // TODO: complete with others from DOI: 10.1021/pr3007045 - // A Systematic Investigation into the Nature of Tryptic HCD Spectra - + // see DOI: 10.1021/pr3007045 A Systematic Investigation into the Nature of Tryptic HCD Spectra static const double imY = EmpiricalFormula("C8H10NO").getMonoWeight(); // 85% static const double imW = EmpiricalFormula("C10H11N2").getMonoWeight(); // 84% static const double imF = EmpiricalFormula("C8H10N").getMonoWeight(); // 84% static const double imL = EmpiricalFormula("C5H12N").getMonoWeight(); // I/L 76% static const double imH = EmpiricalFormula("C5H8N3").getMonoWeight(); // 70% static const double imC = EmpiricalFormula("C2H6NS").getMonoWeight(); // CaC 61% -// static const double imQ = EmpiricalFormula("?").getMonoWeight(); // 52% -// static const double imE = EmpiricalFormula("?").getMonoWeight(); // 37% -// static const double imN = EmpiricalFormula("?").getMonoWeight(); // 11% -// static const double imD = EmpiricalFormula("?").getMonoWeight(); // 4% -// static const double imM = EmpiricalFormula("?").getMonoWeight(); // 3% static const double imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); // 2% - static const double imP = EmpiricalFormula("C4H8N").getMonoWeight(); //? + static const double imQ = 101.0715; // 52% + static const double imE = 102.0555; // 37% + static const double imM = 104.0534; // 3% +// static const double imN = 87.05584; // 11% +// static const double imD = 88.03986; // 4% if (iip.Y) { @@ -655,7 +718,15 @@ class OpenNuXL : } if (iip.M) { - match_one_peak_z1(104.05285, im_MIC); + match_one_peak_z1(imM, im_MIC); + } + if (iip.Q) + { + match_one_peak_z1(imQ, im_MIC); + } + if (iip.E) + { + match_one_peak_z1(imE, im_MIC); } im_MIC /= TIC; @@ -854,6 +925,9 @@ class OpenNuXL : static const double imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); static const double imK2 = EmpiricalFormula("C5H10N1").getMonoWeight(); static const double imK3 = EmpiricalFormula("C6H13N2O").getMonoWeight(); + static const double imQ = 101.0715; + static const double imE = 102.0555; + static const double imM = 104.0534; for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { @@ -895,7 +969,15 @@ class OpenNuXL : } if (iip.M) { - match_one_peak_z1(104.05285 + fa.mass, plss_im_MIC); + match_one_peak_z1(imM + fa.mass, plss_im_MIC); + } + if (iip.Q) + { + match_one_peak_z1(imQ + fa.mass, plss_im_MIC); + } + if (iip.E) + { + match_one_peak_z1(imE + fa.mass, plss_im_MIC); } } plss_im_MIC /= TIC; @@ -1039,7 +1121,7 @@ static void scoreShiftedFragments_( // deisotope Deisotoper::deisotopeAndSingleCharge(spec, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - "decreasing", + "none", 1, 3, false, 2, 10, @@ -2074,7 +2156,20 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("NuXL:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses - ph.setMetaValue(String("NuXL:NA"), *mod_combinations_it->second.begin()); // return first nucleotide formula matching the index of the empirical formula + String NA = *mod_combinations_it->second.begin(); + ph.setMetaValue(String("NuXL:NA"), NA); // return first nucleotide formula matching the index of the empirical formula + + // length of oligo + size_t NA_length = NA.find_first_of("+-"); + if (NA_length == std::string::npos) + { + ph.setMetaValue(String("NuXL:NA_length"), NA.size()); + } + else + { + ph.setMetaValue(String("NuXL:NA_length"), NA_length); + } + ph.setMetaValue(String("NuXL:NT"), String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide ph.setMetaValue(String("NuXL:NA_MASS_z0"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight()); // NA uncharged mass via empirical formula ph.setMetaValue(String("NuXL:isXL"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight() > 0); From 7455989f9c40dd7d4d4ddcb090c7839bb84bb8d8 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 19 Jun 2019 14:47:47 +0200 Subject: [PATCH 054/471] before retraining --- src/utils/OpenNuXL.cpp | 101 +++++++++++++++++++++++++++++++---------- 1 file changed, 77 insertions(+), 24 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 814e680fba0..e55a1322cbb 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -148,21 +148,50 @@ struct ImmoniumIonsInPeptide class AnnotatedHit { public: + /* + Slim indices/views to lookup the actual sequence + */ StringView sequence; SignedSize peptide_mod_index = 0; // enumeration index of the non-NA peptide modification Size rna_mod_index = 0; // index of the NA modification - int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment - float mass_error_p = 0; + int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment static constexpr const char UNKNOWN_NUCLEOTIDE = '?'; char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE; /** The main score (score) is a linear combination of (weighted) subscores + + For the fast score (ignoring all shifted peaks) we calculate: + score = 1.0 * total_loss_score + + 1.0 * total_MIC + + 0.333 * mass_error_p; + + For the all-ion score we calculate: + peptides: + score = -6.486416409280039 + + 4.059968526608637 * ah.total_MIC + + 0.5842539236790404 * ah.modds + + 0.21721652155697285 * ah.total_loss_score + + 1.9988345415208777 * ah.mass_error_p; + XLs: + score = -6.648631037190969 + + 0.4688059636415974 * ah.Morph + + 4.0386886051238 * ah.MIC + + 0.5446999629799386 * ah.modds + + 0.25318342707227187 * ah.total_loss_score + + 0.12472562244230834 * ah.partial_loss_score + + 1.2107674392113372 * ah.mass_error_p + + 2.3319284783288805 * ah.pl_MIC; */ float score = 0; + /** + Normalized precursor mass error score. + */ + float mass_error_p = 0; + // // Scores exclusively calculated from peaks without nucleotide shifts: // @@ -425,15 +454,22 @@ class OpenNuXL : registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); } + /* + @param N number of theoretical peaks + @param peak_in_spectrum number of experimental peaks + @param matched_size number of matched theoretical peaks + */ static double matchOddsScore_( - const Size& N, + const Size& N, + const float fragment_mass_tolerance_Da, + const Size peaks_in_spectrum, + const float mass_range_Da, const Size matched_size) { if (matched_size < 1 || N < 1) { return 0; } - // TODO: try p = Nd/w (number of peaks in spectrum * fragment mass tolerance in Da / MS/MS mass range in Da - see phoshoRS) - - const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see ThresholdMower) + // Nd/w (number of peaks in spectrum * fragment mass tolerance in Da / MS/MS mass range in Da - see phoshoRS) + const double p = peaks_in_spectrum * fragment_mass_tolerance_Da / mass_range_Da; const double pscore = boost::math::ibeta(matched_size + 1, N - matched_size, p); if (pscore <= std::numeric_limits::min()) return -log10(std::numeric_limits::min()); const double minusLog10p1pscore = -log10(pscore); @@ -732,8 +768,14 @@ class OpenNuXL : // if we only have 1 peak assume some kind of average error to not underestimate the real error to much err = Morph > 2 ? err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - modds = matchOddsScore_(total_loss_template_z1_b_ions.size() - + total_loss_template_z1_y_ions.size(), (int)Morph); + + const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000; + + modds = matchOddsScore_(total_loss_template_z1_b_ions.size() + total_loss_template_z1_y_ions.size(), + fragment_mass_tolerance_Da, + exp_spectrum.size(), + exp_spectrum.back().getMZ(), + (int)Morph); } static void scoreShiftedLadderIons_( @@ -984,30 +1026,35 @@ class OpenNuXL : // if we only have 1 peak assume some kind of average error to not underestimate the real error to much plss_err = plss_Morph > 2 ? plss_err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - plss_modds = matchOddsScore_(partial_loss_template_z1_b_ions.size() - + partial_loss_template_z1_y_ions.size(), (int)plss_Morph); + + const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000; + + plss_modds = matchOddsScore_( + partial_loss_template_z1_b_ions.size() + partial_loss_template_z1_y_ions.size(), + fragment_mass_tolerance_Da, + exp_spectrum.size(), + exp_spectrum.back().getMZ(), + (int)plss_Morph); } +/* +* Combine subscores of all-ion scoring. +*/ static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) { if (!isXL) { - return - 6.486416409280039 - + 4.059968526608637 * ah.total_MIC - + 0.5842539236790404 * ah.modds - + 0.21721652155697285 * ah.total_loss_score - + 1.9988345415208777 * ah.mass_error_p; + return + + 1.0 * ah.total_loss_score + + 1.0 * ah.total_MIC + + 1.0 * ah.mass_error_p; } else { - return - 6.648631037190969 - + 0.4688059636415974 * ah.Morph - + 4.0386886051238 * ah.MIC - + 0.5446999629799386 * ah.modds - + 0.25318342707227187 * ah.total_loss_score - + 0.12472562244230834 * ah.partial_loss_score - + 1.2107674392113372 * ah.mass_error_p - + 2.3319284783288805 * ah.pl_MIC; + return + + 1.0 * ah.total_loss_score + + 1.0 * ah.total_MIC + + 1.0 * ah.mass_error_p; } } @@ -3370,7 +3417,13 @@ static void scoreShiftedFragments_( // if we only have 1 peak assume some kind of average error to not underestimate the real error to much plss_err = plss_Morph > 2 ? pl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; - plss_modds = matchOddsScore_(pl_spec->size(), (int)plss_Morph); + + const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; + plss_modds = matchOddsScore_(pl_spec->size(), + fragment_mass_tolerance_Da, + exp_spectrum.size(), + exp_spectrum.back().getMZ(), + (int)plss_Morph); } #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; From 37db6705ddc32e32163f09637c01657697e055be Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 21 Jun 2019 13:53:30 +0200 Subject: [PATCH 055/471] [NOP] some refactoring --- src/utils/OpenNuXL.cpp | 58 +++++++++++++++++++++--------------------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index e55a1322cbb..8d8a9c33957 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -189,6 +189,12 @@ class AnnotatedHit /** Normalized precursor mass error score. + Mass error is assumed normally distributed with: + - mean = 0 + - sd = sqrt(precursor_mass_tolerance) => variance = precursor tolerance + Background error (false hits) is assumed uniform in precursor tolerance window. + mass_error_prior_negatives = 1.0 / (2.0 * precursor_mass_tolerance); + mass_error_p = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; */ float mass_error_p = 0; @@ -454,6 +460,16 @@ class OpenNuXL : registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); } + + // bad score or less then two peaks matching and less than 1% explained signal + static bool badTotalLossScore(float hyperScore, float tlss_Morph, float tlss_modds, float tlss_total_MIC) + { + return (hyperScore < MIN_HYPERSCORE + || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 + || tlss_modds < 1e-10 + || tlss_total_MIC < 0.01); + } + /* @param N number of theoretical peaks @param peak_in_spectrum number of experimental peaks @@ -1047,14 +1063,14 @@ class OpenNuXL : return + 1.0 * ah.total_loss_score + 1.0 * ah.total_MIC - + 1.0 * ah.mass_error_p; + + 0.333 * ah.mass_error_p; } else { return + 1.0 * ah.total_loss_score - + 1.0 * ah.total_MIC - + 1.0 * ah.mass_error_p; + + 1.0 * (ah.MIC + ah.immonium_score + ah.precursor_score) + + 0.333 * ah.mass_error_p; } } @@ -2427,16 +2443,10 @@ static void scoreShiftedFragments_( im_MIC ); - const double total_MIC = tlss_MIC + im_MIC + pc_MIC; + const double tlss_total_MIC = tlss_MIC + im_MIC + pc_MIC; - // super bad score - if (total_loss_score < MIN_HYPERSCORE - || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_modds < 1e-10 - || total_MIC < 0.01) - { - return; - } + // early-out if super bad score + if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { return; } const double mass_error_ppm = (current_peptide_mass - exp_pc_mass) / exp_pc_mass * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; @@ -2455,7 +2465,7 @@ static void scoreShiftedFragments_( ah.immonium_score = im_MIC; ah.precursor_score = pc_MIC; - ah.total_MIC = total_MIC; + ah.total_MIC = tlss_total_MIC; ah.rna_mod_index = rna_mod_idx; ah.isotope_error = isotope_error; @@ -2469,7 +2479,7 @@ static void scoreShiftedFragments_( } // simple combined score in fast scoring: - ah.score = total_loss_score + ah.total_MIC + mass_error_score / 3.0; + ah.score = total_loss_score + tlss_total_MIC + mass_error_score / 3.0; #ifdef DEBUG_OpenNuXL LOG_DEBUG << "best score in pre-score: " << score << endl; @@ -2957,13 +2967,8 @@ static void scoreShiftedFragments_( im_MIC ); - // bad score or less then two peaks matching - if (hyperScore < MIN_HYPERSCORE - || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_MIC < 0.01) - { - continue; - } + const double tlss_total_MIC = tlss_MIC + im_MIC + pc_MIC; + if (badTotalLossScore(hyperScore, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) @@ -2981,7 +2986,7 @@ static void scoreShiftedFragments_( ah.total_loss_score = hyperScore; ah.immonium_score = im_MIC; ah.precursor_score = pc_MIC; - ah.total_MIC = tlss_MIC + im_MIC + pc_MIC; + ah.total_MIC = tlss_total_MIC; ah.rna_mod_index = rna_mod_index; ah.isotope_error = isotope_error; @@ -3101,13 +3106,8 @@ static void scoreShiftedFragments_( im_MIC ); - // bad score or less then two peaks matching - if (hyperScore < MIN_HYPERSCORE - || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_MIC < 0.01) - { - continue; - } + const double tlss_total_MIC = tlss_MIC + im_MIC + pc_MIC; + if (badTotalLossScore(hyperScore, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } float plss_MIC(0), plss_err(1.0), From 90786b29846fdcd767dbd1cc99c7c9629586f6be Mon Sep 17 00:00:00 2001 From: MatthewThe Date: Fri, 21 Jun 2019 16:29:25 +0200 Subject: [PATCH 056/471] [FIX] Fixed Percolator PTM notation and default svm score --- src/topp/PercolatorAdapter.cpp | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/src/topp/PercolatorAdapter.cpp b/src/topp/PercolatorAdapter.cpp index a63039058cf..148637e29e3 100644 --- a/src/topp/PercolatorAdapter.cpp +++ b/src/topp/PercolatorAdapter.cpp @@ -497,7 +497,8 @@ class PercolatorAdapter : sequence += aa_before; sequence += "."; - sequence += hit.getSequence().toString(); + // Percolator uses square brackets to indicate PTMs + sequence += hit.getSequence().toBracketString(false, true); sequence += "."; sequence += aa_after; @@ -1061,7 +1062,7 @@ class PercolatorAdapter : //check each PeptideHit for compliance with one of the PercolatorResults (by sequence) for (vector::iterator hit = it->getHits().begin(); hit != it->getHits().end(); ++hit) { - String peptide_sequence = hit->getSequence().toString(); + String peptide_sequence = hit->getSequence().toBracketString(false, true); String psm_identifier = scan_identifier + peptide_sequence; writeDebug_("PSM identifier in PeptideHit: " + psm_identifier, 10); @@ -1090,8 +1091,15 @@ class PercolatorAdapter : } else { - OPENMS_LOG_WARN << "Identifier " << psm_identifier << " not found in peptide map." << endl; - hit->setMetaValue("MS:1001492", 0.0); // svm score + // If the input contains multiple PSMs per spectrum, Percolator only reports the top scoring PSM. + // The remaining PSMs should be reported as not identified + writeDebug_("PSM identifier " + psm_identifier + " not found in peptide map", 10); + + // Percolator's svm score is scaled such that 0.0 is the score at the chosen FDR threshold, + // with positive scores representing PSMs under the FDR threshold (i.e. identified) + // and negative scores PSMs above the FDR threshold (i.e. not identified); + // -100.0 is typically more than low enough to represent a confidently non-identified PSM. + hit->setMetaValue("MS:1001492", -100.0); // svm score hit->setMetaValue("MS:1001491", 1.0); // percolator q value hit->setMetaValue("MS:1001493", 1.0); // percolator pep @@ -1101,7 +1109,7 @@ class PercolatorAdapter : } else if (scoreType == "svm") { - hit->setScore(0.0); // set SVM score to 0.0 if hit not found in results + hit->setScore(-100.0); // set SVM score to -100.0 if hit not found in results } } } From 50b12c298ff47d5206969a9dfd33b71f683d0800 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 24 Jun 2019 12:40:27 +0200 Subject: [PATCH 057/471] [FIX] move mod to metavalue (5238) --- .../source/ANALYSIS/RNPXL/RNPxlReport.cpp | 11 ++++--- src/topp/PercolatorAdapter.cpp | 14 +++++++-- src/utils/OpenNuXL.cpp | 30 +++++++++++++------ 3 files changed, 39 insertions(+), 16 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp index d67bfc7dcd0..e4a67807d04 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp @@ -243,6 +243,8 @@ namespace OpenMS ph.setMetaValue("NuXL:z4 mass", (double)weight_z4); csv_rows.push_back(row); + +/* // In the last annotation step we add the oligo as delta mass modification // to get the proper theoretical mass annotated in the PeptideHit // Try to add it to the C- then N-terminus. @@ -254,12 +256,12 @@ namespace OpenMS if (!aa.hasCTerminalModification()) { - aa = AASequence::fromString(seq + ".[" + String(rna_weight) + "]"); + aa = AASequence::fromString(seq + ".[" + String(rna_weight + Residue::getInternalToCTerm().getMonoWeight()) + "]"); ph.setSequence(aa); } else if (!aa.hasNTerminalModification()) { - aa = AASequence::fromString("[" + String(rna_weight) + "]." + seq); + aa = AASequence::fromString("[" + String(rna_weight + Residue::getInternalToNTerm().getMonoWeight()) + "]." + seq); ph.setSequence(aa); } else // place it anywhere @@ -269,14 +271,15 @@ namespace OpenMS { if (!a.isModified()) { - aa.setModification(index, "[" + String(rna_weight) + "]"); + aa.setModification(index, "[+" + String(rna_weight) + "]"); break; } ++index; } ph.setSequence(aa); } - } + } +*/ } } } diff --git a/src/topp/PercolatorAdapter.cpp b/src/topp/PercolatorAdapter.cpp index 807da45ef6d..bd3b8d9aa63 100644 --- a/src/topp/PercolatorAdapter.cpp +++ b/src/topp/PercolatorAdapter.cpp @@ -449,9 +449,17 @@ class PercolatorAdapter : int charge = hit.getCharge(); String unmodified_sequence = hit.getSequence().toUnmodifiedString(); - - double calc_mass = hit.getSequence().getMonoWeight(Residue::Full, charge)/charge; - hit.setMetaValue("CalcMass", calc_mass); + + double calc_mass; + if (!hit.metaValueExists("CalcMass")) + { + calc_mass = hit.getSequence().getMonoWeight(Residue::Full, charge)/charge; + hit.setMetaValue("CalcMass", calc_mass); + } + else + { + calc_mass = hit.getMetaValue("CalcMass"); + } if (hit.metaValueExists("IsotopeError")) // MSGFPlus { diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 8d8a9c33957..61a44f0ac6b 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -466,7 +466,7 @@ class OpenNuXL : { return (hyperScore < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 - || tlss_modds < 1e-10 +// || tlss_modds < 1e-10 || tlss_total_MIC < 0.01); } @@ -485,7 +485,9 @@ class OpenNuXL : if (matched_size < 1 || N < 1) { return 0; } // Nd/w (number of peaks in spectrum * fragment mass tolerance in Da / MS/MS mass range in Da - see phoshoRS) - const double p = peaks_in_spectrum * fragment_mass_tolerance_Da / mass_range_Da; + //const double p = peaks_in_spectrum * fragment_mass_tolerance_Da / mass_range_Da; + + const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see ThresholdMower) const double pscore = boost::math::ibeta(matched_size + 1, N - matched_size, p); if (pscore <= std::numeric_limits::min()) return -log10(std::numeric_limits::min()); const double minusLog10p1pscore = -log10(pscore); @@ -1062,15 +1064,15 @@ class OpenNuXL : { return + 1.0 * ah.total_loss_score - + 1.0 * ah.total_MIC - + 0.333 * ah.mass_error_p; +/* + 1.0 * ah.total_MIC + + 0.333 * ah.mass_error_p*/; } else { return - + 1.0 * ah.total_loss_score + + 1.0 * ah.total_loss_score /* + 1.0 * (ah.MIC + ah.immonium_score + ah.precursor_score) - + 0.333 * ah.mass_error_p; + + 0.333 * ah.mass_error_p*/; } } @@ -2222,11 +2224,19 @@ static void scoreShiftedFragments_( String NA = *mod_combinations_it->second.begin(); ph.setMetaValue(String("NuXL:NA"), NA); // return first nucleotide formula matching the index of the empirical formula + double na_mass_z0 = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); // NA uncharged mass via empirical formula // length of oligo size_t NA_length = NA.find_first_of("+-"); if (NA_length == std::string::npos) { - ph.setMetaValue(String("NuXL:NA_length"), NA.size()); + if (na_mass_z0 > 0) + { + ph.setMetaValue(String("NuXL:NA_length"), NA.size()); + } + else + { + ph.setMetaValue(String("NuXL:NA_length"), 0); + } } else { @@ -2234,8 +2244,8 @@ static void scoreShiftedFragments_( } ph.setMetaValue(String("NuXL:NT"), String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide - ph.setMetaValue(String("NuXL:NA_MASS_z0"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight()); // NA uncharged mass via empirical formula - ph.setMetaValue(String("NuXL:isXL"), EmpiricalFormula(mod_combinations_it->first).getMonoWeight() > 0); + ph.setMetaValue(String("NuXL:NA_MASS_z0"), na_mass_z0); // NA uncharged mass via empirical formula + ph.setMetaValue(String("NuXL:isXL"), na_mass_z0 > 0); ph.setMetaValue(String("NuXL:isPhospho"), is_phospho); ph.setMetaValue(String("NuXL:best_localization_score"), ah.best_localization_score); @@ -2254,6 +2264,7 @@ static void scoreShiftedFragments_( ph.setMetaValue("isotope_error", static_cast(ah.isotope_error)); ph.setMetaValue(String("NuXL:ladder_score"), ah.ladder_score); ph.setMetaValue(String("NuXL:sequence_score"), ah.sequence_score); + ph.setMetaValue(String("CalcMass"), + (fixed_and_variable_modified_peptide.getMonoWeight(Residue::Full, charge) + na_mass_z0)/charge); // overwrites CalcMass in PercolatorAdapter ph.setMetaValue("rank", rank); // set the amino acid sequence (for complete loss spectra this is just the variable and modified peptide. For partial loss spectra it additionally contains the loss induced modification) ph.setSequence(fixed_and_variable_modified_peptide); @@ -2319,6 +2330,7 @@ static void scoreShiftedFragments_( << "NuXL:pl_im_MIC" << "NuXL:total_MIC" << "NuXL:NA_MASS_z0" + << "NuXL:NA_length" << "NuXL:ladder_score" << "NuXL:sequence_score" << "precursor_intensity_log10"; From f8b7159c6a3d0174d1f1752a39a8f4d4816858f8 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 24 Jun 2019 13:06:44 +0200 Subject: [PATCH 058/471] one-hot of xl nucleotide --- src/utils/OpenNuXL.cpp | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 61a44f0ac6b..b8e7aea04c0 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -2252,6 +2252,20 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("NuXL:localization_scores"), ah.localization_scores); ph.setMetaValue(String("NuXL:best_localization"), ah.best_localization); + // one-hot encoding of cross-linked nucleotide + const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); + for (const auto& c : can_cross_link) + { + if (c == ah.cross_linked_nucleotide) + { + ph.setMetaValue(String("NuXL:XL_" + String(c)), 1); + } + else + { + ph.setMetaValue(String("NuXL:XL_" + String(c)), 0); + } + } + // also annotate PI to hit so it is available to percolator ph.setMetaValue("precursor_intensity_log10", precursor_intensity_log10); @@ -2337,6 +2351,12 @@ static void scoreShiftedFragments_( if (!purities.empty()) feature_set << "precursor_purity"; + // one-hot encoding of cross-linked nucleotide + const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); + for (const auto& c : can_cross_link) + { + feature_set << String("NuXL:XL_" + String(c)); + } search_parameters.setMetaValue("feature_extractor", "TOPP_PSMFeatureExtractor"); search_parameters.setMetaValue("extra_features", ListUtils::concatenate(feature_set, ",")); From f5c604347057a1486471a7a81d7e50841c065a8e Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 24 Jun 2019 14:48:28 +0200 Subject: [PATCH 059/471] more doc, 5288 --- src/utils/OpenNuXL.cpp | 70 +++++++++++++++++++++++++++++++++++++++--- 1 file changed, 65 insertions(+), 5 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index b8e7aea04c0..fe884ff710e 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -105,6 +105,19 @@ using namespace OpenMS; using namespace OpenMS::Internal; using namespace std; +/* + + + + + + + + + +*/ + + // stores which residues (known to give rise to immonium ions) are in the sequence struct ImmoniumIonsInPeptide { @@ -211,6 +224,19 @@ class AnnotatedHit /** The matched ion current in immonium (immonium_score) and precursor ions (precursor_score) without any nucleotide shift. + + see DOI: 10.1021/pr3007045 A Systematic Investigation into the Nature of Tryptic HCD Spectra + imY = EmpiricalFormula("C8H10NO").getMonoWeight(); // 85% + imW = EmpiricalFormula("C10H11N2").getMonoWeight(); // 84% + imF = EmpiricalFormula("C8H10N").getMonoWeight(); // 84% + imL = EmpiricalFormula("C5H12N").getMonoWeight(); // I/L 76% + imH = EmpiricalFormula("C5H8N3").getMonoWeight(); // 70% + imC = EmpiricalFormula("C2H6NS").getMonoWeight(); // CaC 61% + imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); // 2% + imP = EmpiricalFormula("C4H8N").getMonoWeight(); //? + imQ = 101.0715; // 52% + imE = 102.0555; // 37% + imM = 104.0534; // 3% */ float immonium_score = 0; float precursor_score = 0; @@ -224,8 +250,7 @@ class AnnotatedHit float Morph = 0; /** - The match odds score (modds), uses a cumulativ binomial distribution to calculate the odds - of observing that many matched peaks by chance. + The match odds (-log10) of observing this number of b-,a-, and y-ions assuming a uniform distribution of noise peaks. */ float modds = 0; @@ -234,21 +259,56 @@ class AnnotatedHit // /** - The partial loss score is the X!Tandem HyperScore calculated from b-,y-ions - with nucleotide shifts. + The partial loss score is the X!Tandem HyperScore calculated from b-,a-, and y-ions + with nucleotide shifts. Matches from b- and a-ions are combined, i.e. a matching a_n-ion is counted as b_n-ion. + For a precursor with charge N, all fragment ion charges up to N-1 are considered. + + Calculation of HyperScore: + yFact = logfactorial_(y_ion_count); + bFact = logfactorial_(b_ion_count); + hyperScore = log1p(dot_product) + yFact + bFact; */ float partial_loss_score = 0; /** - The matched ion current (pl_MIC), average fragment error (pl_err), and morpheus score (pl_Morph) are calculated + The matched ion current (pl_MIC) of ladder ions, average fragment error (pl_err), and morpheus score (pl_Morph) are calculated from b-,y-,a-ions with nucleotide shift. Morph: number of matched peaks + the fraction of MIC */ float pl_MIC = 0; float pl_err = 0; float pl_Morph = 0; + + /* + The match odds (-log10) of observing this number of b-,a-, and y-ions with nucleotide shifts assuming a uniform distribution of noise peaks. + */ float pl_modds = 0; + + /* + The MIC of precursor with all nucleotide shifts. + Three variants: No additional loss, loss of water, and loss ammonia. + Charge states considered: 1..N (precursor charge) + */ float pl_pc_MIC = 0; + + /** + The matched ion current calculated from immonium ions with nucleotide shifts. + Only singly charged immonium ions are considered. + + imY = EmpiricalFormula("C8H10NO").getMonoWeight(); + imW = EmpiricalFormula("C10H11N2").getMonoWeight(); + imF = EmpiricalFormula("C8H10N").getMonoWeight(); + imH = EmpiricalFormula("C5H8N3").getMonoWeight(); + imC = EmpiricalFormula("C2H6NS").getMonoWeight(); + imP = EmpiricalFormula("C4H8N").getMonoWeight(); + imL = EmpiricalFormula("C5H12N").getMonoWeight(); + imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); + imK2 = EmpiricalFormula("C5H10N1").getMonoWeight(); + imK3 = EmpiricalFormula("C6H13N2O").getMonoWeight(); + imQ = 101.0715; + imE = 102.0555; + imM = 104.0534; + */ float pl_im_MIC = 0; // From cdebb986f30fbfefcd2784f16ec6c325cdf0f45e Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 25 Jun 2019 17:14:26 +0200 Subject: [PATCH 060/471] pseudo reverse database, keep top n scores of XLs and non-XLs --- src/utils/OpenNuXL.cpp | 905 +++++++++++++++++++++++------------------ 1 file changed, 501 insertions(+), 404 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index fe884ff710e..79be30003c6 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -105,19 +105,6 @@ using namespace OpenMS; using namespace OpenMS::Internal; using namespace std; -/* - - - - - - - - - -*/ - - // stores which residues (known to give rise to immonium ions) are in the sequence struct ImmoniumIonsInPeptide { @@ -1136,6 +1123,13 @@ class OpenNuXL : } } + static float calculateFastScore(const AnnotatedHit& ah) + { + return + + 1.0 * ah.total_loss_score +/* + 1.0 * ah.total_MIC + + 0.333 * ah.mass_error_p*/; + } /* * Score fragments carrying NA adducts . */ @@ -1317,22 +1311,31 @@ static void scoreShiftedFragments_( } } - /* @brief Localization step of the cross-link identification engine. - * Given a top scoring candidate (based on total loss spectrum) it: - * - generates all fragment adducts based on the attached precursor adduct - * - annotated peaks - * - calculates an additive score that considers the presence or absence of evidence for a cross-linking site - * - the maximum score is reported - */ - void postScoreHits_(const PeakMap& exp, - vector >& annotated_hits, - Size top_hits, - const RNPxlModificationMassesResult& mm, - const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, - const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, - Size max_variable_mods_per_peptide, - double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, - const RNPxlParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts) + void filterTopNAnnotations_(vector>& ahs, const Size top_hits) + { +#ifdef _OPENMP +#pragma omp parallel for +#endif + for (SignedSize scan_index = 0; scan_index < (SignedSize)ahs.size(); ++scan_index) + { + // sort and keeps n best elements according to score + const Size topn = top_hits > ahs[scan_index].size() ? ahs[scan_index].size() : top_hits; + std::partial_sort(ahs[scan_index].begin(), ahs[scan_index].begin() + topn, ahs[scan_index].end(), AnnotatedHit::hasBetterScore); + ahs[scan_index].resize(topn); + ahs[scan_index].shrink_to_fit(); + } + } + + void rescoreFastHits_( + const PeakMap& exp, + vector>& annotated_hits, + const RNPxlModificationMassesResult& mm, + const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, + const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, + Size max_variable_mods_per_peptide, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const RNPxlParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts) { TheoreticalSpectrumGenerator partial_loss_spectrum_generator; auto param = partial_loss_spectrum_generator.getParameters(); @@ -1348,198 +1351,199 @@ static void scoreShiftedFragments_( param.setValue("add_y_ions", "true"); param.setValue("add_z_ions", "false"); partial_loss_spectrum_generator.setParameters(param); - - assert(exp.size() == annotated_hits.size()); - - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << exp.size() << " : " << annotated_hits.size() << endl; - #endif - - // remove all but top n scoring for localization (usually all but the first one) #ifdef _OPENMP -#pragma omp parallel for +#pragma omp parallel for #endif for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) { - // sort and keeps n best elements according to score - const Size topn = top_hits > annotated_hits[scan_index].size() ? annotated_hits[scan_index].size() : top_hits; - std::partial_sort(annotated_hits[scan_index].begin(), annotated_hits[scan_index].begin() + topn, annotated_hits[scan_index].end(), AnnotatedHit::hasBetterScore); - annotated_hits[scan_index].resize(topn); - annotated_hits[scan_index].shrink_to_fit(); - } + vector new_hits; - // If we did a (total-loss) only fast scoring, PSMs were not associated with a nucleotide. - // To make the localization code work for both fast and slow (all-shifts) scoring, - // we copy PSMs for every cross-linkable nucleotide present in the precursor. - // Then we recalculate the XL specific scores not conisdered in fast scoring - if (fast_scoring_) - { -#ifdef _OPENMP -#pragma omp parallel for -#endif - for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) + // for each PSM of this spectrum + for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) { - vector new_hits; - - // for each PSM of this spectrum - for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) + // determine NA on precursor from index in map + auto mod_combinations_it = mm.mod_combinations.begin(); + std::advance(mod_combinations_it, annotated_hits[scan_index][i].rna_mod_index); + const String precursor_rna_adduct = *mod_combinations_it->second.begin(); + const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; + + if (precursor_rna_adduct == "none") { - // determine NA on precursor from index in map - auto mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, annotated_hits[scan_index][i].rna_mod_index); - const String precursor_rna_adduct = *mod_combinations_it->second.begin(); - const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; - - if (precursor_rna_adduct == "none") - { - new_hits.push_back(annotated_hits[scan_index][i]); - } - else + new_hits.push_back(annotated_hits[scan_index][i]); + } + else + { + // if we have a cross-link, copy PSM information for each cross-linkable nucleotides + for (auto const & c : feasible_MS2_adducts) { - // if we have a cross-link, copy PSM information for each cross-linkable nucleotides - for (auto const & c : feasible_MS2_adducts) - { - AnnotatedHit a(annotated_hits[scan_index][i]); - a.cross_linked_nucleotide = c.first; // nucleotide - new_hits.push_back(a); - } + AnnotatedHit a(annotated_hits[scan_index][i]); + a.cross_linked_nucleotide = c.first; // nucleotide + new_hits.push_back(a); } } - annotated_hits[scan_index].swap(new_hits); } + annotated_hits[scan_index].swap(new_hits); + } - // fill in values of slow scoring so they can be used in percolator - for (Size scan_index = 0; scan_index != annotated_hits.size(); ++scan_index) + // fill in values of slow scoring so they can be used in percolator + for (Size scan_index = 0; scan_index != annotated_hits.size(); ++scan_index) + { + // for each PSM of this spectrum + for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) { - // for each PSM of this spectrum - for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) - { - AnnotatedHit& ah = annotated_hits[scan_index][i]; - - // reconstruct fixed and variable modified peptide sequence (without NA) - const String& unmodified_sequence = ah.sequence.getString(); - AASequence aas = AASequence::fromString(unmodified_sequence); - vector all_modified_peptides; - ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications, aas); - ModifiedPeptideGenerator::applyVariableModifications(variable_modifications, aas, max_variable_mods_per_peptide, all_modified_peptides); - AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; - double current_peptide_mass_without_NA = fixed_and_variable_modified_peptide.getMonoWeight(); + AnnotatedHit& ah = annotated_hits[scan_index][i]; - // determine NA on precursor from index in map - auto mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, ah.rna_mod_index); - const String precursor_rna_adduct = *mod_combinations_it->second.begin(); - const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; - const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; - const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); + // reconstruct fixed and variable modified peptide sequence (without NA) + const String& unmodified_sequence = ah.sequence.getString(); + AASequence aas = AASequence::fromString(unmodified_sequence); + vector all_modified_peptides; + ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications, aas); + ModifiedPeptideGenerator::applyVariableModifications(variable_modifications, aas, max_variable_mods_per_peptide, all_modified_peptides); + AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; + double current_peptide_mass_without_NA = fixed_and_variable_modified_peptide.getMonoWeight(); - if (precursor_rna_adduct == "none") - { - ah.score = OpenNuXL::calculateCombinedScore(ah, false); - continue; - } + // determine NA on precursor from index in map + auto mod_combinations_it = mm.mod_combinations.begin(); + std::advance(mod_combinations_it, ah.rna_mod_index); + const String precursor_rna_adduct = *mod_combinations_it->second.begin(); + const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; + const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; + const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); - // determine current nucleotide and associated partial losses - vector partial_loss_modification; - for (auto const & nuc_2_adducts : feasible_MS2_adducts) + if (precursor_rna_adduct == "none") + { + ah.score = OpenNuXL::calculateCombinedScore(ah, false); + continue; + } + + // determine current nucleotide and associated partial losses + vector partial_loss_modification; + for (auto const & nuc_2_adducts : feasible_MS2_adducts) + { + if (nuc_2_adducts.first == ah.cross_linked_nucleotide) { - if (nuc_2_adducts.first == ah.cross_linked_nucleotide) - { - partial_loss_modification = nuc_2_adducts.second; - } + partial_loss_modification = nuc_2_adducts.second; } + } - // TODO: not needed to generate all templates (but will make not much of a difference - // as this is only done a few thousand times during post-scoring). That way, - // the code is basically the same as in the main scoring loop. - PeakSpectrum partial_loss_template_z1, - partial_loss_template_z2, - partial_loss_template_z3; - - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); + // TODO: not needed to generate all templates (but will make not much of a difference + // as this is only done a few thousand times during post-scoring). That way, + // the code is basically the same as in the main scoring loop. + PeakSpectrum partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3; + + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); - PeakSpectrum marker_ions_sub_score_spectrum_z1, - partial_loss_spectrum_z1, - partial_loss_spectrum_z2; + PeakSpectrum marker_ions_sub_score_spectrum_z1, + partial_loss_spectrum_z1, + partial_loss_spectrum_z2; - // nucleotide is associated with certain NA-related fragment losses? - if (!partial_loss_modification.empty()) - { - // shifted b- / y- / a-ions - // generate shifted_immonium_ions_sub_score_spectrum.empty - RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - current_peptide_mass_without_NA, - precursor_rna_adduct, - precursor_rna_mass, - 1, - partial_loss_modification, - partial_loss_template_z1, - partial_loss_template_z2, - partial_loss_template_z3, - partial_loss_spectrum_z1); - - RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - current_peptide_mass_without_NA, - precursor_rna_adduct, - precursor_rna_mass, - 2, // don't know the charge of the precursor at that point - partial_loss_modification, - partial_loss_template_z1, - partial_loss_template_z2, - partial_loss_template_z3, - partial_loss_spectrum_z2); - } + // nucleotide is associated with certain NA-related fragment losses? + if (!partial_loss_modification.empty()) + { + // shifted b- / y- / a-ions + // generate shifted_immonium_ions_sub_score_spectrum.empty + RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, + current_peptide_mass_without_NA, + precursor_rna_adduct, + precursor_rna_mass, + 1, + partial_loss_modification, + partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3, + partial_loss_spectrum_z1); + + RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, + current_peptide_mass_without_NA, + precursor_rna_adduct, + precursor_rna_mass, + 2, // don't know the charge of the precursor at that point + partial_loss_modification, + partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3, + partial_loss_spectrum_z2); + } - // add shifted marker ions - marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation - RNPxlFragmentIonGenerator::addMS2MarkerIons( - marker_ions, - marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0], - marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); - - const PeakSpectrum& exp_spectrum = exp[scan_index]; - float partial_loss_sub_score(0), - marker_ions_sub_score(0), - plss_MIC(0), - plss_err(1.0), - plss_Morph(0), - plss_modds(0); - - postScorePartialLossFragments_( unmodified_sequence.size(), - exp_spectrum, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - partial_loss_spectrum_z1, - partial_loss_spectrum_z2, - marker_ions_sub_score_spectrum_z1, - partial_loss_sub_score, - marker_ions_sub_score, - plss_MIC, - plss_err, - plss_Morph, - plss_modds); - - - // fill in missing scores not considered in fast scoring - ah.pl_MIC = plss_MIC; - ah.pl_err = plss_err; - ah.pl_Morph = plss_Morph; - ah.pl_modds = plss_modds; - // add extra matched ion current - ah.total_MIC += plss_MIC; - // scores from shifted peaks - ah.marker_ions_score = marker_ions_sub_score; - ah.partial_loss_score = partial_loss_sub_score; - // combined score - ah.score = OpenNuXL::calculateCombinedScore(ah, true); - } + // add shifted marker ions + marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation + RNPxlFragmentIonGenerator::addMS2MarkerIons( + marker_ions, + marker_ions_sub_score_spectrum_z1, + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0], + marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); + + const PeakSpectrum& exp_spectrum = exp[scan_index]; + float partial_loss_sub_score(0), + marker_ions_sub_score(0), + plss_MIC(0), + plss_err(1.0), + plss_Morph(0), + plss_modds(0); + +//TODO: dieser Teil ist anders + postScorePartialLossFragments_( unmodified_sequence.size(), + exp_spectrum, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + partial_loss_spectrum_z1, + partial_loss_spectrum_z2, + marker_ions_sub_score_spectrum_z1, + partial_loss_sub_score, + marker_ions_sub_score, + plss_MIC, + plss_err, + plss_Morph, + plss_modds); + + + // fill in missing scores not considered in fast scoring + ah.pl_MIC = plss_MIC; + ah.pl_err = plss_err; + ah.pl_Morph = plss_Morph; + ah.pl_modds = plss_modds; + // add extra matched ion current +// TODO: dieser Teil ist anders + ah.total_MIC += plss_MIC; + // scores from shifted peaks + ah.marker_ions_score = marker_ions_sub_score; + ah.partial_loss_score = partial_loss_sub_score; + // combined score + ah.score = OpenNuXL::calculateCombinedScore(ah, true); } - } + } + } + void annotateAndLocate_( + const PeakMap& exp, + vector>& annotated_hits, + const RNPxlModificationMassesResult& mm, + const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, + const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, + Size max_variable_mods_per_peptide, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const RNPxlParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts) + { + TheoreticalSpectrumGenerator partial_loss_spectrum_generator; + auto param = partial_loss_spectrum_generator.getParameters(); + param.setValue("add_first_prefix_ion", "true"); + param.setValue("add_abundant_immonium_ions", "false"); // we add them manually for charge 1 + param.setValue("add_precursor_peaks", "true"); + param.setValue("add_all_precursor_charges", "false"); // we add them manually for every charge + param.setValue("add_metainfo", "true"); + param.setValue("add_a_ions", "true"); + param.setValue("add_b_ions", "true"); + param.setValue("add_c_ions", "false"); + param.setValue("add_x_ions", "false"); + param.setValue("add_y_ions", "true"); + param.setValue("add_z_ions", "false"); + partial_loss_spectrum_generator.setParameters(param); #ifdef _OPENMP #pragma omp parallel for #endif @@ -2162,199 +2166,261 @@ static void scoreShiftedFragments_( } } - /// Filter by top scoring hits, reconstruct original peptide from memory efficient structure, and add additional meta information. - void postProcessHits_(const PeakMap& exp, - vector >& annotated_hits, - vector& protein_ids, - vector& peptide_ids, - Size top_hits, + /* @brief Localization step of the cross-link identification engine. + 1. Generates all fragment adducts based on the attached precursor adduct + 2. Calculates an additive score that considers the presence or absence of evidence for a cross-linking site + 3. Add additional meta information for PSM. + */ + void postScoreHits_(const PeakMap& exp, + vector >& annotated_XL_hits, + vector >& annotated_peptide_hits, + const RNPxlModificationMassesResult& mm, + const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, + const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, + Size max_variable_mods_per_peptide, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const RNPxlParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts) + { + assert(exp.size() == annotated_XL_hits.size()); + assert(exp.size() == annotated_peptide_hits.size()); + + // If we did a (total-loss) only fast scoring, PSMs were not associated with a nucleotide. + // To make the localization code work for both fast and slow (all-shifts) scoring, + // we copy PSMs for every cross-linkable nucleotide present in the precursor. + // Then we recalculate the XL specific scores not conisdered in fast scoring + if (fast_scoring_) + { + rescoreFastHits_(exp, annotated_XL_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); + rescoreFastHits_(exp, annotated_peptide_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); + } + + annotateAndLocate_(exp, annotated_XL_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); + annotateAndLocate_(exp, annotated_peptide_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); + } + + void fillSpectrumID_( + const vector& ahs, + PeptideIdentification& pi, const RNPxlModificationMassesResult& mm, const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, - Size max_variable_mods_per_peptide, + const Size max_variable_mods_per_peptide, + const Size scan_index, + const MSSpectrum& spec, const vector& purities) { - // remove all but top n scoring (Note: this is currently necessary as postScoreHits_ might reintroduce nucleotide specific hits for fast scoring) -#ifdef _OPENMP -#pragma omp parallel for -#endif - for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) + pi.setMetaValue("scan_index", static_cast(scan_index)); + pi.setMetaValue("spectrum_reference", spec.getNativeID()); + pi.setScoreType("NuXLScore"); + pi.setHigherScoreBetter(true); + pi.setRT(spec.getRT()); + pi.setMZ(spec.getPrecursors()[0].getMZ()); + double precursor_intensity_log10 = log10(1.0 + spec.getPrecursors()[0].getIntensity()); + pi.setMetaValue("precursor_intensity_log10", precursor_intensity_log10); + Size charge = spec.getPrecursors()[0].getCharge(); + + // create full peptide hit structure from annotated hits + vector phs = pi.getHits(); + for (auto const & ah : ahs) + { + PeptideHit ph; + ph.setCharge(charge); + + // get unmodified string + const String & s = ah.sequence.getString(); + + OPENMS_POSTCONDITION(!s.empty(), "Error: empty sequence in annotated hits."); + AASequence aas = AASequence::fromString(s); + + // reapply modifications (because for memory reasons we only stored the index and recreation is fast) + vector all_modified_peptides; + ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications, aas); + ModifiedPeptideGenerator::applyVariableModifications(variable_modifications, aas, max_variable_mods_per_peptide, all_modified_peptides); + + // reannotate much more memory heavy AASequence object + AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; + ph.setScore(ah.score); + ph.setMetaValue(String("NuXL:score"), ah.score); // important for Percolator feature set because the PeptideHit score might be overwritten by a q-value + + // - # of variable mods + // - Phosphopeptide + int is_phospho(0); + int n_var_mods = 0; + for (Size i = 0; i != fixed_and_variable_modified_peptide.size(); ++i) + { + const Residue& r = fixed_and_variable_modified_peptide[i]; + if (!r.isModified()) continue; + if (variable_modifications.val.find(r.getModification()) != variable_modifications.val.end()) + { + ++n_var_mods; + } + + if (r.getModification()->getId() == "Phospho") { is_phospho = 1; } + } + auto n_term_mod = fixed_and_variable_modified_peptide.getNTerminalModification(); + auto c_term_mod = fixed_and_variable_modified_peptide.getCTerminalModification(); + + if (n_term_mod != nullptr && + variable_modifications.val.find(n_term_mod) != variable_modifications.val.end()) ++n_var_mods; + if (c_term_mod != nullptr && + variable_modifications.val.find(c_term_mod) != variable_modifications.val.end()) ++n_var_mods; + + ph.setMetaValue(String("variable_modifications"), n_var_mods); + + + // determine NA modification from index in map + std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); + std::advance(mod_combinations_it, ah.rna_mod_index); + ph.setMetaValue(String("NuXL:mass_error_p"), ah.mass_error_p); + ph.setMetaValue(String("NuXL:total_loss_score"), ah.total_loss_score); + ph.setMetaValue(String("NuXL:immonium_score"), ah.immonium_score); + ph.setMetaValue(String("NuXL:precursor_score"), ah.precursor_score); + ph.setMetaValue(String("NuXL:marker_ions_score"), ah.marker_ions_score); + ph.setMetaValue(String("NuXL:partial_loss_score"), ah.partial_loss_score); + + // total loss and partial loss (pl) related subscores (matched ion current, avg. fragment error, morpheus score) + ph.setMetaValue(String("NuXL:MIC"), ah.MIC); + ph.setMetaValue(String("NuXL:err"), ah.err); + ph.setMetaValue(String("NuXL:Morph"), ah.Morph); + ph.setMetaValue(String("NuXL:modds"), ah.modds); + ph.setMetaValue(String("NuXL:pl_MIC"), ah.pl_MIC); + ph.setMetaValue(String("NuXL:pl_err"), ah.pl_err); + ph.setMetaValue(String("NuXL:pl_Morph"), ah.pl_Morph); + ph.setMetaValue(String("NuXL:pl_modds"), ah.pl_modds); + ph.setMetaValue(String("NuXL:pl_pc_MIC"), ah.pl_pc_MIC); + ph.setMetaValue(String("NuXL:pl_im_MIC"), ah.pl_im_MIC); + + ph.setMetaValue(String("NuXL:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses + + String NA = *mod_combinations_it->second.begin(); + ph.setMetaValue(String("NuXL:NA"), NA); // return first nucleotide formula matching the index of the empirical formula + + double na_mass_z0 = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); // NA uncharged mass via empirical formula + // length of oligo + size_t NA_length = NA.find_first_of("+-"); + if (NA_length == std::string::npos) { - // sort and keeps n best elements according to score - Size topn = top_hits > annotated_hits[scan_index].size() ? annotated_hits[scan_index].size() : top_hits; - std::partial_sort(annotated_hits[scan_index].begin(), annotated_hits[scan_index].begin() + topn, annotated_hits[scan_index].end(), AnnotatedHit::hasBetterScore); - annotated_hits[scan_index].resize(topn); - annotated_hits.shrink_to_fit(); + if (na_mass_z0 > 0) + { + ph.setMetaValue(String("NuXL:NA_length"), NA.size()); + } + else + { + ph.setMetaValue(String("NuXL:NA_length"), 0); + } + } + else + { + ph.setMetaValue(String("NuXL:NA_length"), NA_length); } -#ifdef _OPENMP -#pragma omp parallel for -#endif - for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) - { - const MSSpectrum& spec = exp[scan_index]; - if (!annotated_hits[scan_index].empty()) + ph.setMetaValue(String("NuXL:NT"), String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide + ph.setMetaValue(String("NuXL:NA_MASS_z0"), na_mass_z0); // NA uncharged mass via empirical formula + ph.setMetaValue(String("NuXL:isXL"), na_mass_z0 > 0); + ph.setMetaValue(String("NuXL:isPhospho"), is_phospho); + + ph.setMetaValue(String("NuXL:best_localization_score"), ah.best_localization_score); + ph.setMetaValue(String("NuXL:localization_scores"), ah.localization_scores); + ph.setMetaValue(String("NuXL:best_localization"), ah.best_localization); + + // one-hot encoding of cross-linked nucleotide + const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); + for (const auto& c : can_cross_link) { - // create empty PeptideIdentification object and fill meta data - PeptideIdentification pi; - pi.setMetaValue("scan_index", static_cast(scan_index)); - pi.setMetaValue("spectrum_reference", spec.getNativeID()); - pi.setScoreType("NuXLScore"); - pi.setHigherScoreBetter(true); - pi.setRT(spec.getRT()); - pi.setMZ(spec.getPrecursors()[0].getMZ()); - double precursor_intensity_log10 = log10(1.0 + spec.getPrecursors()[0].getIntensity()); - pi.setMetaValue("precursor_intensity_log10", precursor_intensity_log10); - Size charge = spec.getPrecursors()[0].getCharge(); - - // create full peptide hit structure from annotated hits - vector phs; - size_t rank(0); - for (auto const & ah : annotated_hits[scan_index]) + if (c == ah.cross_linked_nucleotide) + { + ph.setMetaValue(String("NuXL:XL_" + String(c)), 1); + } + else { - PeptideHit ph; - ph.setCharge(charge); - - // get unmodified string - const String & s = ah.sequence.getString(); - - OPENMS_POSTCONDITION(!s.empty(), "Error: empty sequence in annotated hits."); - AASequence aas = AASequence::fromString(s); - - // reapply modifications (because for memory reasons we only stored the index and recreation is fast) - vector all_modified_peptides; - ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications, aas); - ModifiedPeptideGenerator::applyVariableModifications(variable_modifications, aas, max_variable_mods_per_peptide, all_modified_peptides); - - // reannotate much more memory heavy AASequence object - AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; - ph.setScore(ah.score); - ph.setMetaValue(String("NuXL:score"), ah.score); // important for Percolator feature set because the PeptideHit score might be overwritten by a q-value - - // - # of variable mods - // - Phosphopeptide - int is_phospho(0); - int n_var_mods = 0; - for (Size i = 0; i != fixed_and_variable_modified_peptide.size(); ++i) - { - const Residue& r = fixed_and_variable_modified_peptide[i]; - if (!r.isModified()) continue; - if (variable_modifications.val.find(r.getModification()) != variable_modifications.val.end()) - { - ++n_var_mods; - } + ph.setMetaValue(String("NuXL:XL_" + String(c)), 0); + } + } - if (r.getModification()->getId() == "Phospho") { is_phospho = 1; } - } - auto n_term_mod = fixed_and_variable_modified_peptide.getNTerminalModification(); - auto c_term_mod = fixed_and_variable_modified_peptide.getCTerminalModification(); - - if (n_term_mod != nullptr && - variable_modifications.val.find(n_term_mod) != variable_modifications.val.end()) ++n_var_mods; - if (c_term_mod != nullptr && - variable_modifications.val.find(c_term_mod) != variable_modifications.val.end()) ++n_var_mods; - - ph.setMetaValue(String("variable_modifications"), n_var_mods); - - - // determine NA modification from index in map - std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, ah.rna_mod_index); - ph.setMetaValue(String("NuXL:mass_error_p"), ah.mass_error_p); - ph.setMetaValue(String("NuXL:total_loss_score"), ah.total_loss_score); - ph.setMetaValue(String("NuXL:immonium_score"), ah.immonium_score); - ph.setMetaValue(String("NuXL:precursor_score"), ah.precursor_score); - ph.setMetaValue(String("NuXL:marker_ions_score"), ah.marker_ions_score); - ph.setMetaValue(String("NuXL:partial_loss_score"), ah.partial_loss_score); - - // total loss and partial loss (pl) related subscores (matched ion current, avg. fragment error, morpheus score) - ph.setMetaValue(String("NuXL:MIC"), ah.MIC); - ph.setMetaValue(String("NuXL:err"), ah.err); - ph.setMetaValue(String("NuXL:Morph"), ah.Morph); - ph.setMetaValue(String("NuXL:modds"), ah.modds); - ph.setMetaValue(String("NuXL:pl_MIC"), ah.pl_MIC); - ph.setMetaValue(String("NuXL:pl_err"), ah.pl_err); - ph.setMetaValue(String("NuXL:pl_Morph"), ah.pl_Morph); - ph.setMetaValue(String("NuXL:pl_modds"), ah.pl_modds); - ph.setMetaValue(String("NuXL:pl_pc_MIC"), ah.pl_pc_MIC); - ph.setMetaValue(String("NuXL:pl_im_MIC"), ah.pl_im_MIC); - - ph.setMetaValue(String("NuXL:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses - - String NA = *mod_combinations_it->second.begin(); - ph.setMetaValue(String("NuXL:NA"), NA); // return first nucleotide formula matching the index of the empirical formula - - double na_mass_z0 = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); // NA uncharged mass via empirical formula - // length of oligo - size_t NA_length = NA.find_first_of("+-"); - if (NA_length == std::string::npos) - { - if (na_mass_z0 > 0) - { - ph.setMetaValue(String("NuXL:NA_length"), NA.size()); - } - else - { - ph.setMetaValue(String("NuXL:NA_length"), 0); - } - } - else - { - ph.setMetaValue(String("NuXL:NA_length"), NA_length); - } + // also annotate PI to hit so it is available to percolator + ph.setMetaValue("precursor_intensity_log10", precursor_intensity_log10); - ph.setMetaValue(String("NuXL:NT"), String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide - ph.setMetaValue(String("NuXL:NA_MASS_z0"), na_mass_z0); // NA uncharged mass via empirical formula - ph.setMetaValue(String("NuXL:isXL"), na_mass_z0 > 0); - ph.setMetaValue(String("NuXL:isPhospho"), is_phospho); + if (!purities.empty()) + { + ph.setMetaValue("precursor_purity", purities[scan_index].signal_proportion); + } - ph.setMetaValue(String("NuXL:best_localization_score"), ah.best_localization_score); - ph.setMetaValue(String("NuXL:localization_scores"), ah.localization_scores); - ph.setMetaValue(String("NuXL:best_localization"), ah.best_localization); + ph.setPeakAnnotations(ah.fragment_annotations); + ph.setMetaValue("isotope_error", static_cast(ah.isotope_error)); + ph.setMetaValue(String("NuXL:ladder_score"), ah.ladder_score); + ph.setMetaValue(String("NuXL:sequence_score"), ah.sequence_score); + ph.setMetaValue(String("CalcMass"), + (fixed_and_variable_modified_peptide.getMonoWeight(Residue::Full, charge) + na_mass_z0)/charge); // overwrites CalcMass in PercolatorAdapter + // set the amino acid sequence (for complete loss spectra this is just the variable and modified peptide. For partial loss spectra it additionally contains the loss induced modification) + ph.setSequence(fixed_and_variable_modified_peptide); + phs.push_back(ph); // add new hit + } - // one-hot encoding of cross-linked nucleotide - const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); - for (const auto& c : can_cross_link) - { - if (c == ah.cross_linked_nucleotide) - { - ph.setMetaValue(String("NuXL:XL_" + String(c)), 1); - } - else - { - ph.setMetaValue(String("NuXL:XL_" + String(c)), 0); - } - } + pi.setHits(phs); + pi.assignRanks(); - // also annotate PI to hit so it is available to percolator - ph.setMetaValue("precursor_intensity_log10", precursor_intensity_log10); + // assign (unique) ranks + phs = pi.getHits(); + for (Size r = 0; r != phs.size(); ++r) { phs[r].setMetaValue("rank", static_cast(r)); } + pi.setHits(phs); + } - if (!purities.empty()) - { - ph.setMetaValue("precursor_purity", purities[scan_index].signal_proportion); - } - ph.setPeakAnnotations(ah.fragment_annotations); - ph.setMetaValue("isotope_error", static_cast(ah.isotope_error)); - ph.setMetaValue(String("NuXL:ladder_score"), ah.ladder_score); - ph.setMetaValue(String("NuXL:sequence_score"), ah.sequence_score); - ph.setMetaValue(String("CalcMass"), + (fixed_and_variable_modified_peptide.getMonoWeight(Residue::Full, charge) + na_mass_z0)/charge); // overwrites CalcMass in PercolatorAdapter - ph.setMetaValue("rank", rank); - // set the amino acid sequence (for complete loss spectra this is just the variable and modified peptide. For partial loss spectra it additionally contains the loss induced modification) - ph.setSequence(fixed_and_variable_modified_peptide); - phs.push_back(ph); - ++rank; - } + /** + 1. Reconstruct original peptide from memory efficient structure + 2. Add additional meta information for PSM. + */ + void postProcessHits_(const PeakMap& exp, + vector >& annotated_XL_hits, + vector >& annotated_peptide_hits, + vector& protein_ids, + vector& peptide_ids, + const RNPxlModificationMassesResult& mm, + const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, + const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, + Size max_variable_mods_per_peptide, + const vector& purities) + { + assert(annotated_XL_hits.size() == annotated_peptide_hits.size()); + SignedSize hit_count = static_cast(annotated_XL_hits.size()); - pi.setHits(phs); - pi.assignRanks(); + for (SignedSize scan_index = 0; scan_index < hit_count; ++scan_index) + { + const MSSpectrum& spec = exp[scan_index]; + vector& ahs_XL = annotated_XL_hits[scan_index]; + vector& ahs_peptide = annotated_peptide_hits[scan_index]; -#ifdef _OPENMP -#pragma omp critical (peptide_ids_access) -#endif - { - peptide_ids.push_back(std::move(pi)); - } + if (ahs_XL.empty() && ahs_peptide.empty()) continue; + + // create empty PeptideIdentification object and fill meta data + peptide_ids.push_back(PeptideIdentification()); + + if (!ahs_XL.empty()) + { + fillSpectrumID_( + ahs_XL, + peptide_ids.back(), // append hits + mm, + fixed_modifications, + variable_modifications, + max_variable_mods_per_peptide, + scan_index, + spec, + purities); + } + + if (!ahs_peptide.empty()) + { + fillSpectrumID_( + ahs_peptide, + peptide_ids.back(), // append hits + mm, + fixed_modifications, + variable_modifications, + max_variable_mods_per_peptide, + scan_index, + spec, + purities); } } @@ -2565,13 +2631,13 @@ static void scoreShiftedFragments_( auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); ah.ladder_score = ladderScore_(range) / (double)intensity_sum.size(); range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); - if (range.second != range.first) // see Macot Percolator paper + if (range.second != range.first) // see Mascot Percolator paper { ah.sequence_score = ladderScore_(range) / (double)intensity_sum.size(); } // simple combined score in fast scoring: - ah.score = total_loss_score + tlss_total_MIC + mass_error_score / 3.0; + ah.score = calculateFastScore(ah); #ifdef DEBUG_OpenNuXL LOG_DEBUG << "best score in pre-score: " << score << endl; @@ -2856,13 +2922,16 @@ static void scoreShiftedFragments_( // preallocate storage for PSMs - vector > annotated_hits(spectra.size(), vector()); - for (auto & a : annotated_hits) { a.reserve(2 * report_top_hits); } - + vector > annotated_XLs(spectra.size(), vector()); + for (auto & a : annotated_XLs) { a.reserve(2 * report_top_hits); } + vector > annotated_peptides(spectra.size(), vector()); + for (auto & a : annotated_peptides) { a.reserve(2 * report_top_hits); } #ifdef _OPENMP // locking is done at the spectrum level to ensure good parallelisation - vector annotated_hits_lock(annotated_hits.size()); - for (size_t i = 0; i != annotated_hits_lock.size(); i++) { omp_init_lock(&(annotated_hits_lock[i])); } + vector annotated_XLs_lock(annotated_XLs.size()); + for (size_t i = 0; i != annotated_XLs_lock.size(); i++) { omp_init_lock(&(annotated_XLs_lock[i])); } + vector annotated_peptides_lock(annotated_peptides.size()); + for (size_t i = 0; i != annotated_peptides_lock.size(); i++) { omp_init_lock(&(annotated_peptides_lock[i])); } #endif // load fasta file @@ -2875,6 +2944,9 @@ static void scoreShiftedFragments_( // generate decoy protein sequences by reversing them if (generate_decoys) { + ProteaseDigestion digestor; + digestor.setEnzyme(getStringOption_("peptide:enzyme")); + digestor.setMissedCleavages(0); // for decoy generation disable missed cleavages progresslogger.startProgress(0, 1, "Generate decoys..."); // append decoy proteins @@ -2882,7 +2954,20 @@ static void scoreShiftedFragments_( for (size_t i = 0; i != old_size; ++i) { FASTAFile::FASTAEntry e = fasta_db[i]; - e.sequence.reverse(); + + std::vector output; + digestor.digest(AASequence::fromString(e.sequence), output); + + // pseudo reverse protein digest + e.sequence = ""; + for (const auto & aas : output) + { + std::string s = aas.toUnmodifiedString(); + auto last = --s.end(); + std::reverse(s.begin(), last); + e.sequence += s; + } + e.identifier = "DECOY_" + e.identifier; fasta_db.push_back(e); } @@ -2892,6 +2977,8 @@ static void scoreShiftedFragments_( progresslogger.endProgress(); } + + // set up enzyme const Size missed_cleavages = getIntOption_("peptide:missed_cleavages"); ProteaseDigestion digestor; digestor.setEnzyme(getStringOption_("peptide:enzyme")); @@ -3099,20 +3186,20 @@ static void scoreShiftedFragments_( #endif #ifdef _OPENMP - omp_set_lock(&(annotated_hits_lock[scan_index])); + omp_set_lock(&(annotated_peptides_lock[scan_index])); #endif { - annotated_hits[scan_index].emplace_back(move(ah)); + annotated_peptides[scan_index].emplace_back(move(ah)); // prevent vector from growing indefinitly (memory) but don't shrink the vector every time - if (annotated_hits[scan_index].size() >= 2 * report_top_hits) + if (annotated_peptides[scan_index].size() >= 2 * report_top_hits) { - std::partial_sort(annotated_hits[scan_index].begin(), annotated_hits[scan_index].begin() + report_top_hits, annotated_hits[scan_index].end(), AnnotatedHit::hasBetterScore); - annotated_hits[scan_index].resize(report_top_hits); + std::partial_sort(annotated_peptides[scan_index].begin(), annotated_peptides[scan_index].begin() + report_top_hits, annotated_peptides[scan_index].end(), AnnotatedHit::hasBetterScore); + annotated_peptides[scan_index].resize(report_top_hits); } } #ifdef _OPENMP - omp_unset_lock(&(annotated_hits_lock[scan_index])); + omp_unset_lock(&(annotated_peptides_lock[scan_index])); #endif } } @@ -3141,7 +3228,6 @@ static void scoreShiftedFragments_( const char& cross_linked_nucleotide = nuc_2_adducts.first; const vector& partial_loss_modification = nuc_2_adducts.second; - PeakSpectrum marker_ions_sub_score_spectrum_z1; // add shifted marker ions marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation @@ -3286,20 +3372,20 @@ static void scoreShiftedFragments_( #endif #ifdef _OPENMP - omp_set_lock(&(annotated_hits_lock[scan_index])); + omp_set_lock(&(annotated_XLs_lock[scan_index])); #endif { - annotated_hits[scan_index].emplace_back(move(ah)); + annotated_XLs[scan_index].emplace_back(move(ah)); // prevent vector from growing indefinitly (memory) but don't shrink the vector every time - if (annotated_hits[scan_index].size() >= 2 * report_top_hits) + if (annotated_XLs[scan_index].size() >= 2 * report_top_hits) { - std::partial_sort(annotated_hits[scan_index].begin(), annotated_hits[scan_index].begin() + report_top_hits, annotated_hits[scan_index].end(), AnnotatedHit::hasBetterScore); - annotated_hits[scan_index].resize(report_top_hits); + std::partial_sort(annotated_XLs[scan_index].begin(), annotated_XLs[scan_index].begin() + report_top_hits, annotated_XLs[scan_index].end(), AnnotatedHit::hasBetterScore); + annotated_XLs[scan_index].resize(report_top_hits); } } #ifdef _OPENMP - omp_unset_lock(&(annotated_hits_lock[scan_index])); + omp_unset_lock(&(annotated_XLs_lock[scan_index])); #endif } } // for every nucleotide in the precursor @@ -3313,7 +3399,7 @@ static void scoreShiftedFragments_( const int & isotope_error = l->second.second; const double & exp_pc_mass = l->first; - // generate PSMs for spectrum[scan_index] and add them to annotated_hits[scan_index] + // generate PSMs for spectrum[scan_index] and add them to annotated hits addPSMsTotalLossScoring_( spectra[scan_index], *cit, // string view on unmodified sequence @@ -3330,9 +3416,9 @@ static void scoreShiftedFragments_( mass_error_prior_negatives, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - annotated_hits[scan_index], + annotated_peptides[scan_index], #ifdef _OPENMP - annotated_hits_lock[scan_index], + annotated_peptides_lock[scan_index], #endif report_top_hits ); @@ -3371,9 +3457,16 @@ static void scoreShiftedFragments_( progresslogger.startProgress(0, 1, "localization..."); + assert(exp.size() == annotated_XLss.size()); + assert(exp.size() == annotated_peptides.size()); + + // remove all but top n scoring for localization (usually all but the first one) + filterTopNAnnotations_(annotated_XLs, report_top_hits); + filterTopNAnnotations_(annotated_peptides, report_top_hits); + postScoreHits_(spectra, - annotated_hits, - report_top_hits, + annotated_XLs, + annotated_peptides, mm, fixed_modifications, variable_modifications, @@ -3383,11 +3476,17 @@ static void scoreShiftedFragments_( all_feasible_fragment_adducts); progresslogger.startProgress(0, 1, "Post-processing and annotation..."); + + // remove all but top n scoring PSMs again + // Note: this is currently necessary as postScoreHits_ might reintroduce nucleotide specific hits for fast scoring + filterTopNAnnotations_(annotated_XLs, report_top_hits); + filterTopNAnnotations_(annotated_peptides, report_top_hits); + postProcessHits_(spectra, - annotated_hits, + annotated_XLs, + annotated_peptides, protein_ids, peptide_ids, - report_top_hits, mm, fixed_modifications, variable_modifications, @@ -3427,10 +3526,7 @@ static void scoreShiftedFragments_( // annotate RNPxl related information to hits and create report vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); - if (generate_decoys) - { - fdr.apply(peptide_ids); - } + if (generate_decoys) { fdr.apply(peptide_ids); } // write ProteinIdentifications and PeptideIdentifications to IdXML IdXMLFile().store(out_idxml, protein_ids, peptide_ids); @@ -3449,7 +3545,8 @@ static void scoreShiftedFragments_( #ifdef _OPENMP // free locks - for (size_t i = 0; i != annotated_hits_lock.size(); i++) { omp_destroy_lock(&(annotated_hits_lock[i])); } + for (size_t i = 0; i != annotated_XLs_lock.size(); i++) { omp_destroy_lock(&(annotated_XLs_lock[i])); } + for (size_t i = 0; i != annotated_peptides_lock.size(); i++) { omp_destroy_lock(&(annotated_peptides_lock[i])); } #endif return EXECUTION_OK; From a90d9f588a783def800dacfa5c518be293d22b62 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 1 Jul 2019 12:30:11 +0200 Subject: [PATCH 061/471] 5370 --- src/utils/OpenNuXL.cpp | 43 +++++++++++++++++++++++++++++++++++------- 1 file changed, 36 insertions(+), 7 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 79be30003c6..f3ab6ed9d3f 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -1107,20 +1107,42 @@ class OpenNuXL : */ static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) { + return -7.9010278 + 0.7545435 * ah.total_loss_score + 3.1219378 * ah.sequence_score + + 0.33 * ah.mass_error_p; +/* + (Intercept) NuXL.total_loss_score NuXL.sequence_score + -7.9010278 0.7545435 3.1219378 +*/ +/* + (Intercept) NuXL.total_loss_score NuXL.modds + -10.2740314 0.7115905 0.6139411 + NuXL.isXL NuXL.pl_modds NuXL.ladder_score + 1.6851418 0.6187959 2.7555106 + + return + + 0.7115905 * ah.total_loss_score + + 0.6139411 * ah.modds + + 1.6851418 * ah.isXL + + 0.6187959 * ah.pl_modds + + 2.7555106 * ah.ladder_score; + // + 1.0 * ah.total_MIC + // + 0.333 * ah.mass_error_p; + if (!isXL) { return + 1.0 * ah.total_loss_score -/* + 1.0 * ah.total_MIC - + 0.333 * ah.mass_error_p*/; + // + 1.0 * ah.total_MIC + // + 0.333 * ah.mass_error_p; } else { return - + 1.0 * ah.total_loss_score /* - + 1.0 * (ah.MIC + ah.immonium_score + ah.precursor_score) - + 0.333 * ah.mass_error_p*/; + + 1.0 * ah.total_loss_score + // + 1.0 * (ah.MIC + ah.immonium_score + ah.precursor_score) + // + 0.333 * ah.mass_error_p; } +*/ } static float calculateFastScore(const AnnotatedHit& ah) @@ -2103,7 +2125,7 @@ static void scoreShiftedFragments_( OPENMS_LOG_DEBUG << String::number(100.0 * sites_sum_score[i], 2); #endif - if (i != 0) localization_scores += ' '; + if (i != 0) localization_scores += ','; if (sites_sum_score[i] > 0 ) { localization_scores += String::number(100.0 * sites_sum_score[i], 2); @@ -2321,7 +2343,14 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("NuXL:isPhospho"), is_phospho); ph.setMetaValue(String("NuXL:best_localization_score"), ah.best_localization_score); - ph.setMetaValue(String("NuXL:localization_scores"), ah.localization_scores); + if (!ah.localization_scores.empty()) + { + ph.setMetaValue(String("NuXL:localization_scores"), ah.localization_scores); + } + else + { + ph.setMetaValue(String("NuXL:localization_scores"), "NA"); + } ph.setMetaValue(String("NuXL:best_localization"), ah.best_localization); // one-hot encoding of cross-linked nucleotide From 18af0f822026badd6175f3c05927b596175bc398 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 1 Jul 2019 20:01:43 +0200 Subject: [PATCH 062/471] sqrt mower, total HS and total Morph score File name: 1-AChernev_080219_dir_HeLa_cyt_slow_UCGA_perc_001_XLs.idXML Number of: runs: 2 protein hits: 343 non-redundant protein hits: 343 (only hits that differ in the accession) matched spectra: 5356 peptide hits: 5356 (avg. length: 14) modified top-hits: 1098/5356 (20.5%) non-redundant peptide hits: 630 (only hits that differ in sequence and/or modifications) Modification count (top-hits only): Carbamyl 624, Carbamyl (K) 119, Oxidation (M) 489 File name: 1-AChernev_080219_dir_HeLa_cyt_slow_UCGA_001_XLs.idXML Number of: runs: 1 protein hits: 267 non-redundant protein hits: 267 (only hits that differ in the accession) matched spectra: 3787 peptide hits: 3787 (avg. length: 15) modified top-hits: 807/3787 (21.300000000000001%) non-redundant peptide hits: 454 (only hits that differ in sequence and/or modifications) Modification count (top-hits only): Carbamyl 463, Carbamyl (K) 63, Oxidation (M) 377 --- src/tests/topp/CMakeLists.txt | 10 ++++ src/utils/OpenNuXL.cpp | 86 +++++++++++++++++++++++++++-------- 2 files changed, 78 insertions(+), 18 deletions(-) diff --git a/src/tests/topp/CMakeLists.txt b/src/tests/topp/CMakeLists.txt index 7f607679339..254bab7e00b 100644 --- a/src/tests/topp/CMakeLists.txt +++ b/src/tests/topp/CMakeLists.txt @@ -1746,6 +1746,16 @@ ${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_inp add_test("TOPP_OpenNuXL_5_out1" ${DIFF} -whitelist "IdentificationRun date" "db=" -in1 OpenNuXL_5_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_5_output.idXML ) set_tests_properties("TOPP_OpenNuXL_5_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_5") + +# reporting of multiple hits and tsv output and decoy generation with huge mass window so that all candidates are scored +add_test("TOPP_OpenNuXL_6" ${TOPP_BIN_PATH}/OpenNuXL -test -in +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -RNPxl:decoys -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_6_output.tmp -report:top_hits 2 -out_tsv OpenNuXL_6_output2.tmp -precursor:mass_tolerance 1e9 -RNPxl:scoring slow) +add_test("TOPP_OpenNuXL_6_out1" ${DIFF} -whitelist "IdentificationRun date" +"db=" -in1 OpenNuXL_6_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_6_output.idXML ) +add_test("TOPP_OpenNuXL_6_out2" ${DIFF} -in1 OpenNuXL_6_output2.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_6_output2.tsv ) +set_tests_properties("TOPP_OpenNuXL_6_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_6") +set_tests_properties("TOPP_OpenNuXL_6_out2" PROPERTIES DEPENDS "TOPP_OpenNuXL_6") + #------------------------------------------------------------------------------ # RTModel tests add_test("TOPP_RTModel_1" ${TOPP_BIN_PATH}/RTModel -test -in ${DATA_DIR_TOPP}/RTModel_1_input.idXML -out RTModel_1_output.tmp -ini ${DATA_DIR_TOPP}/RTModel_1_parameters.ini) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index f3ab6ed9d3f..b9c135c6387 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -73,6 +73,7 @@ #include #include #include +#include #include #include @@ -600,6 +601,7 @@ class OpenNuXL : return z; } + // score ions without nucleotide shift static void scorePeptideIons_( const PeakSpectrum& exp_spectrum, const DataArrays::IntegerDataArray& exp_charges, @@ -630,6 +632,8 @@ class OpenNuXL : const Size N = intensity_sum.size(); std::vector b_ions(N, 0.0), y_ions(N, 0.0); + vector peak_matched(exp_spectrum.size(), false); + // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); @@ -653,10 +657,14 @@ class OpenNuXL : // found peak match if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) { - const double intensity = exp_spectrum[index].getIntensity(); - b_mean_err += intensity * std::abs(theo_mz - exp_mz); - dot_product += intensity; - b_ions[i] += intensity; + if (!peak_matched[index]) + { + const double intensity = exp_spectrum[index].getIntensity(); + dot_product += intensity; + b_mean_err += intensity * std::abs(theo_mz - exp_mz); + b_ions[i] += intensity; + peak_matched[index] = true; + } } } } @@ -683,6 +691,15 @@ class OpenNuXL : y_mean_err += intensity * std::abs(theo_mz - exp_mz); dot_product += intensity; y_ions[N-1 - i] += intensity; + + if (!peak_matched[index]) + { + const double intensity = exp_spectrum[index].getIntensity(); + y_mean_err += intensity * std::abs(theo_mz - exp_mz); + dot_product += intensity; + y_ions[N-1 - i] += intensity; + peak_matched[index] = true; + } } } } @@ -749,8 +766,12 @@ class OpenNuXL : // found peak match if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) { - const double intensity = exp_spectrum[index].getIntensity(); - pc_MIC += intensity; + if (!peak_matched[index]) + { + const double intensity = exp_spectrum[index].getIntensity(); + pc_MIC += intensity; + peak_matched[index] = true; + } } } } @@ -766,7 +787,11 @@ class OpenNuXL : if (exp_charges[index] == 1 && std::abs(theo_mz - exp_spectrum[index].getMZ()) < max_dist_dalton) // found peak match { - score += exp_spectrum[index].getIntensity(); + if (!peak_matched[index]) + { + score += exp_spectrum[index].getIntensity(); + peak_matched[index] = true; + } } }; @@ -877,6 +902,8 @@ class OpenNuXL : // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); + vector peak_matched(exp_spectrum.size(), false); + // match b- and a-ions (we record a-ions as b-ions) for (double diff2b : {0.0, -27.994915} ) // b-ion and a-ion ('CO' mass diff from b- to a-ion) { @@ -899,10 +926,14 @@ class OpenNuXL : // found peak match if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) { - const double intensity = exp_spectrum[index].getIntensity(); - b_mean_err += intensity * std::abs(theo_mz - exp_mz); - dot_product += intensity; - b_ions[i] += intensity; + if (!peak_matched[index]) + { + const double intensity = exp_spectrum[index].getIntensity(); + b_mean_err += intensity * std::abs(theo_mz - exp_mz); + dot_product += intensity; + b_ions[i] += intensity; + peak_matched[index] = true; + } } } } @@ -929,10 +960,14 @@ class OpenNuXL : // found peak match if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) { - const double intensity = exp_spectrum[index].getIntensity(); - y_mean_err += intensity * std::abs(theo_mz - exp_mz); - dot_product += intensity; - y_ions[N-1 - i] += intensity; + if (!peak_matched[index]) + { + const double intensity = exp_spectrum[index].getIntensity(); + y_mean_err += intensity * std::abs(theo_mz - exp_mz); + dot_product += intensity; + y_ions[N-1 - i] += intensity; + peak_matched[index] = true; + } } } } @@ -999,8 +1034,12 @@ class OpenNuXL : // found peak match if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) { - const double intensity = exp_spectrum[index].getIntensity(); - plss_pc_MIC += intensity; + if (!peak_matched[index]) + { + const double intensity = exp_spectrum[index].getIntensity(); + plss_pc_MIC += intensity; + peak_matched[index] = true; + } } } } @@ -1018,7 +1057,11 @@ class OpenNuXL : if (exp_charges[index] == 1 && std::abs(theo_mz - exp_spectrum[index].getMZ()) < max_dist_dalton) // found peak match { - score += exp_spectrum[index].getIntensity(); + if (!peak_matched[index]) + { + score += exp_spectrum[index].getIntensity(); + peak_matched[index] = true; + } } }; @@ -1229,6 +1272,9 @@ static void scoreShiftedFragments_( bool single_charge_spectra, bool annotate_charge = false) { + SqrtMower sqrt_mower_filter; + sqrt_mower_filter.filterPeakMap(exp); + // filter MS2 map // remove 0 intensities ThresholdMower threshold_mower_filter; @@ -2312,6 +2358,8 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("NuXL:pl_modds"), ah.pl_modds); ph.setMetaValue(String("NuXL:pl_pc_MIC"), ah.pl_pc_MIC); ph.setMetaValue(String("NuXL:pl_im_MIC"), ah.pl_im_MIC); + ph.setMetaValue(String("NuXL:total_Morph"), ah.Morph + ah.pl_Morph); + ph.setMetaValue(String("NuXL:total_HS"), ah.total_loss_score + ah.partial_loss_score); ph.setMetaValue(String("NuXL:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses @@ -2502,6 +2550,8 @@ static void scoreShiftedFragments_( << "NuXL:NA_length" << "NuXL:ladder_score" << "NuXL:sequence_score" + << "NuXL:total_Morph" + << "NuXL:total_HS" << "precursor_intensity_log10"; if (!purities.empty()) feature_set << "precursor_purity"; From 02255ab4287f6e90553f62a28e2bfda00adfa2d8 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 2 Jul 2019 13:54:26 +0200 Subject: [PATCH 063/471] with tags 5410 / 3787 --- src/utils/OpenNuXL.cpp | 55 ++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 53 insertions(+), 2 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index b9c135c6387..5791a1273fa 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -1263,6 +1263,52 @@ static void scoreShiftedFragments_( if (plss_err > ft_da) plss_err = ft_da; } + void calculateNucleotideTags_(PeakMap& exp, + const double fragment_mass_tolerance, + const bool fragment_mass_tolerance_unit_ppm, + const RNPxlParameterParsing::NucleotideToFragmentAdductMap & nucleotide_to_fragment_adducts) + { + // set of all possibly observable fragment adduct masses + set adduct_mass; + for (const auto & p : nucleotide_to_fragment_adducts) + { + for (const auto & fa : p.second) + { + adduct_mass.insert(fa.mass); + } + } + for (auto & spec : exp) + { + if (spec.getMSLevel() != 2) continue; + // maximum charge considered + const unsigned int max_z = std::min(2U, static_cast(spec.getPrecursors()[0].getCharge() - 1)); + + vector mzs; + for (auto const& p : spec) { mzs.push_back(p.getMZ()); } // faster + + Size match(0); + for (Size i = 0; i != mzs.size(); ++i) + { + for (Size j = i+1; j < mzs.size(); ++j) + { + double m = mzs[j]; + double dm = m - mzs[i]; + for (Size z = 1; z <= max_z; ++z) + { + const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, m) : fragment_mass_tolerance; + auto left = adduct_mass.lower_bound((dm*z) - tolerance); + if (left == adduct_mass.end()) continue; + if (fabs(*left - (dm*z)) < tolerance) ++match; + } + } + } + + spec.getIntegerDataArrays().resize(2); + spec.getIntegerDataArrays()[1].push_back(match); + spec.getIntegerDataArrays()[1].setName("nucleotide_mass_tags"); + } + } + /* @brief Filter spectra to remove noise. Parameter are passed to spectra filter. */ @@ -2423,6 +2469,8 @@ static void scoreShiftedFragments_( ph.setMetaValue("precursor_purity", purities[scan_index].signal_proportion); } + ph.setMetaValue("nucleotide_mass_tags_log10", log10(1.0 + (double)spec.getIntegerDataArrays()[1][0])); + ph.setPeakAnnotations(ah.fragment_annotations); ph.setMetaValue("isotope_error", static_cast(ah.isotope_error)); ph.setMetaValue(String("NuXL:ladder_score"), ah.ladder_score); @@ -2552,8 +2600,8 @@ static void scoreShiftedFragments_( << "NuXL:sequence_score" << "NuXL:total_Morph" << "NuXL:total_HS" - << "precursor_intensity_log10"; - + << "precursor_intensity_log10" + << "nucleotide_mass_tags_log10"; if (!purities.empty()) feature_set << "precursor_purity"; // one-hot encoding of cross-linked nucleotide @@ -2987,6 +3035,8 @@ static void scoreShiftedFragments_( annotate_charge); progresslogger.endProgress(); + calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); + // build multimap of precursor mass to scan index (and perform some mass and length based filtering) using MassToScanMultiMap = multimap>; MassToScanMultiMap multimap_mass_2_scan_index; // map precursor mass to scan index and (potential) isotopic missassignment @@ -3533,6 +3583,7 @@ static void scoreShiftedFragments_( false, // no single charge (false), annotate charge (true) true); + calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); progresslogger.startProgress(0, 1, "localization..."); From f42c82560ed03e18e3dfc22426c64a91d4acf40d Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 3 Jul 2019 17:44:30 +0200 Subject: [PATCH 064/471] good fast scoring --- src/utils/OpenNuXL.cpp | 71 +++++++++++++++++++++++++++--------------- 1 file changed, 46 insertions(+), 25 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 5791a1273fa..0e9b95dcdd6 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -603,7 +603,7 @@ class OpenNuXL : // score ions without nucleotide shift static void scorePeptideIons_( - const PeakSpectrum& exp_spectrum, + const PeakSpectrum& exp_spectrum, const DataArrays::IntegerDataArray& exp_charges, const vector& total_loss_template_z1_b_ions, const vector& total_loss_template_z1_y_ions, @@ -613,6 +613,7 @@ class OpenNuXL : const double fragment_mass_tolerance, const bool fragment_mass_tolerance_unit_ppm, std::vector& intensity_sum, + vector& peak_matched, float& hyperScore, float& MIC, float& Morph, @@ -627,12 +628,13 @@ class OpenNuXL : OPENMS_PRECONDITION(total_loss_template_z1_b_ions.size() > 0, "b- and y-ion arrays must not be empty."); OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_y_ions.size(), "Sum array needs to be of same size as y-ion array"); + OPENMS_PRECONDITION(peak_matched.size() == exp_spectrum.size(), "Peak matched needs to be of same size as experimental spectrum"); + OPENMS_PRECONDITION(std::count_if(peak_matched.begin(), peak_matched.end(), [](bool b){return b == true;}) == 0;, "Peak matched must be initialized to false"); double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); std::vector b_ions(N, 0.0), y_ions(N, 0.0); - vector peak_matched(exp_spectrum.size(), false); // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); @@ -747,6 +749,7 @@ class OpenNuXL : const double bFact = logfactorial_(b_ion_count); hyperScore = log1p(dot_product) + yFact + bFact; MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); + for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum MIC /= TIC; Morph = b_ion_count + y_ion_count + MIC; err = (y_mean_err + b_mean_err)/(b_sum + y_sum); @@ -880,6 +883,7 @@ class OpenNuXL : const PeakSpectrum& exp_spectrum, const DataArrays::IntegerDataArray& exp_charges, std::vector& intensity_sum, + std::vector& peak_matched, float& plss_hyperScore, float& plss_MIC, float& plss_Morph, @@ -902,8 +906,6 @@ class OpenNuXL : // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); - vector peak_matched(exp_spectrum.size(), false); - // match b- and a-ions (we record a-ions as b-ions) for (double diff2b : {0.0, -27.994915} ) // b-ion and a-ion ('CO' mass diff from b- to a-ion) { @@ -1011,6 +1013,7 @@ class OpenNuXL : const double bFact = logfactorial_(b_ion_count); plss_hyperScore = log1p(dot_product) + yFact + bFact; plss_MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); + for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum plss_MIC /= TIC; plss_Morph = b_ion_count + y_ion_count + plss_MIC; plss_err = (y_mean_err + b_mean_err)/(b_sum + y_sum); @@ -1151,7 +1154,7 @@ class OpenNuXL : static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) { return -7.9010278 + 0.7545435 * ah.total_loss_score + 3.1219378 * ah.sequence_score - + 0.33 * ah.mass_error_p; + + 0.33 * ah.mass_error_p + 0.01*ah.total_MIC; /* (Intercept) NuXL.total_loss_score NuXL.sequence_score -7.9010278 0.7545435 3.1219378 @@ -1209,6 +1212,7 @@ static void scoreShiftedFragments_( const vector &partial_loss_template_z1_y_ions, const PeakSpectrum &marker_ions_sub_score_spectrum_z1, vector& intensity_sum, + vector& matched_peaks, float &partial_loss_sub_score, float &marker_ions_sub_score, float &plss_MIC, @@ -1248,6 +1252,7 @@ static void scoreShiftedFragments_( exp_spectrum, exp_spectrum.getIntegerDataArrays()[0], intensity_sum, + matched_peaks, partial_loss_sub_score, plss_MIC, plss_Morph, @@ -1280,11 +1285,11 @@ static void scoreShiftedFragments_( for (auto & spec : exp) { if (spec.getMSLevel() != 2) continue; - // maximum charge considered - const unsigned int max_z = std::min(2U, static_cast(spec.getPrecursors()[0].getCharge() - 1)); - + // faster vector mzs; - for (auto const& p : spec) { mzs.push_back(p.getMZ()); } // faster + vector charges; + for (auto const& p : spec) { mzs.push_back(p.getMZ()); } + for (auto const& p : spec.getIntegerDataArrays()[0]) { charges.push_back(p); } Size match(0); for (Size i = 0; i != mzs.size(); ++i) @@ -1293,13 +1298,13 @@ static void scoreShiftedFragments_( { double m = mzs[j]; double dm = m - mzs[i]; - for (Size z = 1; z <= max_z; ++z) - { - const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, m) : fragment_mass_tolerance; - auto left = adduct_mass.lower_bound((dm*z) - tolerance); - if (left == adduct_mass.end()) continue; - if (fabs(*left - (dm*z)) < tolerance) ++match; - } + + if (charges[i] != charges[j]) continue; + + const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, m) : fragment_mass_tolerance; + auto left = adduct_mass.lower_bound((dm*charges[i]) - tolerance); + if (left == adduct_mass.end()) continue; + if (fabs(*left - (dm*charges[i])) < tolerance ) ++match; } } @@ -1310,7 +1315,16 @@ static void scoreShiftedFragments_( } /* @brief Filter spectra to remove noise. - Parameter are passed to spectra filter. + + - Remove zero intensities + - Scale by root to reduce impact of high-intensity peaks + - Normalize max intensity to 1.0 + - Remove isotopic peaks and determine charge + - Set Unknown charge to z=1. Otherwise we get a lot of spurious matches + - Keep 20 highest-intensity peaks in 100 m/z windows + - Keep max. 400 peaks per spectrum + to highly charged fragments in the low m/z region + - Calculate TIC of filtered spectrum */ void preprocessSpectra_(PeakMap& exp, double fragment_mass_tolerance, @@ -1318,14 +1332,14 @@ static void scoreShiftedFragments_( bool single_charge_spectra, bool annotate_charge = false) { - SqrtMower sqrt_mower_filter; - sqrt_mower_filter.filterPeakMap(exp); - // filter MS2 map // remove 0 intensities ThresholdMower threshold_mower_filter; threshold_mower_filter.filterPeakMap(exp); + SqrtMower sqrt_mower_filter; + sqrt_mower_filter.filterPeakMap(exp); + Normalizer normalizer; normalizer.filterPeakMap(exp); @@ -2707,6 +2721,7 @@ static void scoreShiftedFragments_( im_MIC(0); vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + vector peak_matched(exp_spectrum.size(), false); scorePeptideIons_( exp_spectrum, @@ -2719,6 +2734,7 @@ static void scoreShiftedFragments_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, intensity_sum, + peak_matched, total_loss_score, tlss_MIC, tlss_Morph, @@ -3031,8 +3047,8 @@ static void scoreShiftedFragments_( preprocessSpectra_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - convert_to_single_charge, // no single charge (false), annotate charge (true) - annotate_charge); + convert_to_single_charge, + annotate_charge); progresslogger.endProgress(); calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); @@ -3255,6 +3271,7 @@ static void scoreShiftedFragments_( im_MIC(0); vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + vector peak_matched(exp_spectrum.size(), false); scorePeptideIons_( exp_spectrum, exp_spectrum.getIntegerDataArrays()[0], @@ -3266,6 +3283,7 @@ static void scoreShiftedFragments_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, intensity_sum, + peak_matched, hyperScore, tlss_MIC, tlss_Morph, @@ -3393,6 +3411,8 @@ static void scoreShiftedFragments_( const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + vector peak_matched(exp_spectrum.size(), false); + scorePeptideIons_( exp_spectrum, exp_spectrum.getIntegerDataArrays()[0], @@ -3404,6 +3424,7 @@ static void scoreShiftedFragments_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, intensity_sum, + peak_matched, hyperScore, tlss_MIC, tlss_Morph, @@ -3433,6 +3454,7 @@ static void scoreShiftedFragments_( partial_loss_template_z1_yions, marker_ions_sub_score_spectrum_z1, intensity_sum, + peak_matched, partial_loss_sub_score, marker_ions_sub_score, plss_MIC, @@ -3576,12 +3598,11 @@ static void scoreShiftedFragments_( f.load(in_mzml, spectra); spectra.sortSpectra(true); - // for post scoring don't convert fragments to single charge. Annotate charge instead to every peak. preprocessSpectra_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - false, // no single charge (false), annotate charge (true) - true); + false, // no single charge (false) + true); // annotate charge (true) calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); progresslogger.startProgress(0, 1, "localization..."); From 7dbd5ce359fa13e0e54b49c9077c78d37cbc1901 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 9 Jul 2019 18:53:48 +0200 Subject: [PATCH 065/471] intensity rank --- src/utils/OpenNuXL.cpp | 97 +++++++++++++++++++++--------------------- 1 file changed, 49 insertions(+), 48 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 0e9b95dcdd6..1c2d869445c 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -730,7 +730,6 @@ class OpenNuXL : } } - OPENMS_PRECONDITION(exp_spectrum.getFloatDataArrays().size() == 1, "Exactly one float data array expected."); OPENMS_PRECONDITION(exp_spectrum.getFloatDataArrays()[0].getName() == "TIC", "No TIC stored in spectrum meta data."); OPENMS_PRECONDITION(exp_spectrum.getFloatDataArrays()[0].size() == 1, "Exactly one TIC expected."); @@ -1151,46 +1150,27 @@ class OpenNuXL : /* * Combine subscores of all-ion scoring. */ - static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL) + static float calculateCombinedScore(const AnnotatedHit& ah, + const bool isXL, + const double nucleotide_mass_tags/*, + const double fraction_of_top50annotated*/) { - return -7.9010278 + 0.7545435 * ah.total_loss_score + 3.1219378 * ah.sequence_score - + 0.33 * ah.mass_error_p + 0.01*ah.total_MIC; -/* - (Intercept) NuXL.total_loss_score NuXL.sequence_score - -7.9010278 0.7545435 3.1219378 -*/ -/* - (Intercept) NuXL.total_loss_score NuXL.modds - -10.2740314 0.7115905 0.6139411 - NuXL.isXL NuXL.pl_modds NuXL.ladder_score - 1.6851418 0.6187959 2.7555106 - - return - + 0.7115905 * ah.total_loss_score - + 0.6139411 * ah.modds - + 1.6851418 * ah.isXL - + 0.6187959 * ah.pl_modds - + 2.7555106 * ah.ladder_score; - // + 1.0 * ah.total_MIC - // + 0.333 * ah.mass_error_p; - - if (!isXL) - { - return - + 1.0 * ah.total_loss_score - // + 1.0 * ah.total_MIC - // + 0.333 * ah.mass_error_p; - } - else - { - return - + 1.0 * ah.total_loss_score - // + 1.0 * (ah.MIC + ah.immonium_score + ah.precursor_score) - // + 0.333 * ah.mass_error_p; - } -*/ +// if (ah.Morph + ah.pl_Morph < 5.03) return 0; +// return ah.total_MIC + ah.marker_ions_score + fraction_of_top50annotated; + + return -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err + + 52.2888 * ah.pl_err - 0.0105 * ah.modds + + 88.7997 * ah.immonium_score- 0.88823 * ah.partial_loss_score + 14.2052 * ah.pl_MIC + + 0.61144 * ah.pl_modds + 10.07574543 * ah.pl_pc_MIC -28.05701 * ah.pl_im_MIC + + 2.59655 * ah.total_MIC + 2.38320 * ah.ladder_score + 0.65422535 * (ah.total_loss_score + ah.partial_loss_score); +// 4267 without perc / 5306 with perc auf 1- +// 5010 with perc auf 2- + + +// return -7.9010278 + 0.7545435 * ah.total_loss_score + 3.1219378 * ah.sequence_score + 0.33 * ah.mass_error_p + 0.01*ah.total_MIC; } + static float calculateFastScore(const AnnotatedHit& ah) { return @@ -1291,7 +1271,7 @@ static void scoreShiftedFragments_( for (auto const& p : spec) { mzs.push_back(p.getMZ()); } for (auto const& p : spec.getIntegerDataArrays()[0]) { charges.push_back(p); } - Size match(0); + Size match(0), in_mass_range(0); for (Size i = 0; i != mzs.size(); ++i) { for (Size j = i+1; j < mzs.size(); ++j) @@ -1304,13 +1284,30 @@ static void scoreShiftedFragments_( const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, m) : fragment_mass_tolerance; auto left = adduct_mass.lower_bound((dm*charges[i]) - tolerance); if (left == adduct_mass.end()) continue; + ++in_mass_range; if (fabs(*left - (dm*charges[i])) < tolerance ) ++match; } } + spec.getFloatDataArrays().resize(2); + spec.getFloatDataArrays()[1].push_back((double)match / (double)in_mass_range); + spec.getFloatDataArrays()[1].setName("nucleotide_mass_tags"); + + spec.getIntegerDataArrays().resize(2); - spec.getIntegerDataArrays()[1].push_back(match); - spec.getIntegerDataArrays()[1].setName("nucleotide_mass_tags"); + // calculate ranks + // + // initialize original index locations + vector idx(spec.size()); + std::iota(idx.begin(), idx.end(), 0); + + // sort indexes based on comparing intensity values (0 = highest intensity) + sort(idx.begin(), idx.end(), + [&spec](size_t i1, size_t i2) { return spec[i1].getIntensity() > spec[i2].getIntensity(); }); + + for (int rank : idx) spec.getIntegerDataArrays()[1].push_back(rank); + spec.getIntegerDataArrays()[1].setName("intensity_rank"); + } } @@ -1540,7 +1537,8 @@ static void scoreShiftedFragments_( if (precursor_rna_adduct == "none") { - ah.score = OpenNuXL::calculateCombinedScore(ah, false); + const double tags = exp[scan_index].getFloatDataArrays()[1][0]; + ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); continue; } @@ -1642,7 +1640,8 @@ static void scoreShiftedFragments_( ah.marker_ions_score = marker_ions_sub_score; ah.partial_loss_score = partial_loss_sub_score; // combined score - ah.score = OpenNuXL::calculateCombinedScore(ah, true); + const double tags = exp[scan_index].getFloatDataArrays()[1][0]; + ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); } } } @@ -2483,7 +2482,7 @@ static void scoreShiftedFragments_( ph.setMetaValue("precursor_purity", purities[scan_index].signal_proportion); } - ph.setMetaValue("nucleotide_mass_tags_log10", log10(1.0 + (double)spec.getIntegerDataArrays()[1][0])); + ph.setMetaValue("nucleotide_mass_tags", (double)spec.getFloatDataArrays()[1][0]); ph.setPeakAnnotations(ah.fragment_annotations); ph.setMetaValue("isotope_error", static_cast(ah.isotope_error)); @@ -2615,7 +2614,7 @@ static void scoreShiftedFragments_( << "NuXL:total_Morph" << "NuXL:total_HS" << "precursor_intensity_log10" - << "nucleotide_mass_tags_log10"; + << "nucleotide_mass_tags"; if (!purities.empty()) feature_set << "precursor_purity"; // one-hot encoding of cross-linked nucleotide @@ -3326,7 +3325,8 @@ static void scoreShiftedFragments_( } // combined score - ah.score = OpenNuXL::calculateCombinedScore(ah, false); + const double tags = exp_spectrum.getFloatDataArrays()[1][0]; + ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; @@ -3464,7 +3464,7 @@ static void scoreShiftedFragments_( plss_pc_MIC, plss_im_MIC); - const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC; + const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC + marker_ions_sub_score; /* // less then two shifted peaks? seems to throw out some good hits ??? @@ -3516,7 +3516,8 @@ static void scoreShiftedFragments_( } // combined score - ah.score = OpenNuXL::calculateCombinedScore(ah, true); + const double tags = exp_spectrum.getFloatDataArrays()[1][0]; + ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; From d35b5c4e116bebc66067974d47d9adfc8d194eb7 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 19 Jul 2019 13:44:36 +0200 Subject: [PATCH 066/471] [FIX] make fast scoring more similar to slow scoring --- src/utils/OpenNuXL.cpp | 367 +++++++++++++++++++++++++++++++++++++---- 1 file changed, 338 insertions(+), 29 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1c2d869445c..60c9b44e41c 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -43,6 +43,7 @@ #include #include #include +#include #include #include #include @@ -92,6 +93,7 @@ #include #include +#include #ifdef _OPENMP #include @@ -379,7 +381,9 @@ class OpenNuXL : void registerOptionsAndFlags_() override { registerInputFile_("in", "", "", "input file "); - setValidFormats_("in", ListUtils::create("mzML")); + setValidFormats_("in", ListUtils::create("mzML,raw")); + registerInputFile_("NET_executable", "", "", "The .NET framework executable. Only required on linux and mac.", false, true, ListUtils::create("skipexists")); + registerInputFile_("ThermoRaw_executable", "", "ThermoRawFileParser.exe", "The ThermoRawFileParser executable.", false, true, ListUtils::create("skipexists")); registerInputFile_("database", "", "", "input file "); setValidFormats_("database", ListUtils::create("fasta")); @@ -438,6 +442,18 @@ class OpenNuXL : registerTOPPSubsection_("report", "Reporting Options"); registerIntOption_("report:top_hits", "", 1, "Maximum number of top scoring hits per spectrum that are reported.", false, true); + registerDoubleOption_("report:peptideFDR", "", 0.0, "Maximum q-value of non-cross-linked peptides. (0 = disabled)", false, true); + registerDoubleOption_("report:xlFDR", "", 0.0, "Maximum q-value of cross-linked peptides. (0 = disabled)", false, true); + + registerInputFile_("percolator_executable", "", + // choose the default value according to the platform where it will be executed + #ifdef OPENMS_WINDOWSPLATFORM + "percolator.exe", + #else + "percolator", + #endif + "Percolator executable of the installation e.g. 'percolator.exe'", false, false, ListUtils::create("skipexists")); + // RNPxl specific registerTOPPSubsection_("RNPxl", "RNPxl Options"); @@ -1155,17 +1171,56 @@ class OpenNuXL : const double nucleotide_mass_tags/*, const double fraction_of_top50annotated*/) { -// if (ah.Morph + ah.pl_Morph < 5.03) return 0; + return + 1.0 * ah.total_loss_score; +/* + double score = 2.52872532 + +0.38318303 * nucleotide_mass_tags; + + if (!isXL) + { + score += ah.mass_error_p * 0.45919677 ++ ah.err * 0.01016288 ++ ah.modds * -0.02450589 ++ ah.immonium_score * 0.26555840 ++ ah.precursor_score * 0.06148951 ++ ah.MIC * 0.91845925 ++ ah.sequence_score * 0.23213255 ++ ah.total_loss_score * 8.69880275; + } + else + { +score += ah.mass_error_p * 1.15386068 ++ah.err * -0.75849696 ++ah.pl_err * 0.01731052 ++ah.marker_ions_score * 0.40870416 ++ah.total_loss_score * 4.92806210 ++ah.modds * 0.96869679 ++ah.immonium_score * 0.14292426 ++ah.precursor_score * -0.05822564 ++ah.MIC * 0.73432514 ++ah.pl_MIC * 0.27953670 ++ah.pl_modds * 0.03810840 ++ah.pl_pc_MIC * 0.15083043 ++ah.pl_im_MIC * -0.12681649 ++ah.sequence_score * 0.46228471; + } + + return score; +*/ + +//TODO: check Alex if (ah.Morph + ah.pl_Morph < 5.03) return 0; // return ah.total_MIC + ah.marker_ions_score + fraction_of_top50annotated; - return -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err +/* + return + -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err + 52.2888 * ah.pl_err - 0.0105 * ah.modds + 88.7997 * ah.immonium_score- 0.88823 * ah.partial_loss_score + 14.2052 * ah.pl_MIC + 0.61144 * ah.pl_modds + 10.07574543 * ah.pl_pc_MIC -28.05701 * ah.pl_im_MIC + 2.59655 * ah.total_MIC + 2.38320 * ah.ladder_score + 0.65422535 * (ah.total_loss_score + ah.partial_loss_score); // 4267 without perc / 5306 with perc auf 1- // 5010 with perc auf 2- - +*/ // return -7.9010278 + 0.7545435 * ah.total_loss_score + 3.1219378 * ah.sequence_score + 0.33 * ah.mass_error_p + 0.01*ah.total_MIC; } @@ -1173,8 +1228,7 @@ class OpenNuXL : static float calculateFastScore(const AnnotatedHit& ah) { - return - + 1.0 * ah.total_loss_score + return + 1.0 * ah.total_loss_score /* + 1.0 * ah.total_MIC + 0.333 * ah.mass_error_p*/; } @@ -1635,7 +1689,7 @@ static void scoreShiftedFragments_( ah.pl_modds = plss_modds; // add extra matched ion current // TODO: dieser Teil ist anders - ah.total_MIC += plss_MIC; + ah.total_MIC += plss_MIC + marker_ions_sub_score; // scores from shifted peaks ah.marker_ions_score = marker_ions_sub_score; ah.partial_loss_score = partial_loss_sub_score; @@ -2395,7 +2449,6 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("variable_modifications"), n_var_mods); - // determine NA modification from index in map std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, ah.rna_mod_index); @@ -2585,38 +2638,111 @@ static void scoreShiftedFragments_( */ StringList feature_set; feature_set - << "isotope_error" - << "NuXL:score" - << "variable_modifications" - << "NuXL:isXL" - << "NuXL:isPhospho" << "NuXL:mass_error_p" + << "NuXL:err" << "NuXL:total_loss_score" << "NuXL:modds" << "NuXL:immonium_score" << "NuXL:precursor_score" - << "NuXL:marker_ions_score" - << "NuXL:partial_loss_score" << "NuXL:MIC" - << "NuXL:err" << "NuXL:Morph" + << "NuXL:total_MIC" + << "NuXL:ladder_score" + << "NuXL:sequence_score" + << "NuXL:total_Morph" + << "NuXL:total_HS"; + +#ifdef OPENNUXL_SEPARATE_FEATURES + for (auto & pi : peptide_ids) + { + for (auto & ph : pi.getHits()) + { + if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) + { + ph.setMetaValue("XL_NuXL:mass_error_p", 0.0); + ph.setMetaValue("XL_NuXL:err", 0.0); + ph.setMetaValue("XL_NuXL:total_loss_score",0.0); + ph.setMetaValue("XL_NuXL:modds", 0.0); + ph.setMetaValue("XL_NuXL:immonium_score", 0.0); + ph.setMetaValue("XL_NuXL:precursor_score", 0.0); + ph.setMetaValue("XL_NuXL:MIC", 0.0); + ph.setMetaValue("XL_NuXL:Morph", 0.0); + ph.setMetaValue("XL_NuXL:total_MIC", 0.0); + ph.setMetaValue("XL_NuXL:ladder_score", 0.0); + ph.setMetaValue("XL_NuXL:sequence_score", 0.0); + ph.setMetaValue("XL_NuXL:total_Morph", 0.0); + ph.setMetaValue("XL_NuXL:total_HS", 0.0); + } + else // XL + { + ph.setMetaValue("XL_NuXL:mass_error_p", static_cast(ph.getMetaValue("NuXL:mass_error_p"))); + ph.setMetaValue("XL_NuXL:err", static_cast(ph.getMetaValue("NuXL:err"))); + ph.setMetaValue("XL_NuXL:total_loss_score", static_cast(ph.getMetaValue("NuXL:total_loss_score"))); + ph.setMetaValue("XL_NuXL:modds", static_cast(ph.getMetaValue( "NuXL:modds"))); + ph.setMetaValue("XL_NuXL:immonium_score", static_cast(ph.getMetaValue("NuXL:immonium_score"))); + ph.setMetaValue("XL_NuXL:precursor_score", static_cast(ph.getMetaValue("NuXL:precursor_score"))); + ph.setMetaValue("XL_NuXL:MIC", static_cast(ph.getMetaValue("NuXL:MIC"))); + ph.setMetaValue("XL_NuXL:Morph", static_cast(ph.getMetaValue("NuXL:Morph"))); + ph.setMetaValue("XL_NuXL:total_MIC", static_cast(ph.getMetaValue( "NuXL:total_MIC"))); + ph.setMetaValue("XL_NuXL:ladder_score", static_cast(ph.getMetaValue("NuXL:ladder_score"))); + ph.setMetaValue("XL_NuXL:sequence_score", static_cast(ph.getMetaValue("NuXL:sequence_score"))); + ph.setMetaValue("XL_NuXL:total_Morph", static_cast(ph.getMetaValue("NuXL:total_Morph"))); + ph.setMetaValue("XL_NuXL:total_HS", static_cast(ph.getMetaValue("NuXL:total_HS"))); + + ph.setMetaValue("NuXL:mass_error_p", 0.0); + ph.setMetaValue("NuXL:err", 0.0); + ph.setMetaValue("NuXL:total_loss_score",0.0); + ph.setMetaValue("NuXL:modds", 0.0); + ph.setMetaValue("NuXL:immonium_score", 0.0); + ph.setMetaValue("NuXL:precursor_score", 0.0); + ph.setMetaValue("NuXL:MIC", 0.0); + ph.setMetaValue("NuXL:Morph", 0.0); + ph.setMetaValue("NuXL:total_MIC", 0.0); + ph.setMetaValue("NuXL:ladder_score", 0.0); + ph.setMetaValue("NuXL:sequence_score", 0.0); + ph.setMetaValue("NuXL:total_Morph", 0.0); + ph.setMetaValue("NuXL:total_HS", 0.0); + } + } + } + + feature_set + << "XL_NuXL:mass_error_p" + << "XL_NuXL:err" + << "XL_NuXL:total_loss_score" + << "XL_NuXL:modds" + << "XL_NuXL:immonium_score" + << "XL_NuXL:precursor_score" + << "XL_NuXL:MIC" + << "XL_NuXL:Morph" + << "XL_NuXL:total_MIC" + << "XL_NuXL:ladder_score" + << "XL_NuXL:sequence_score" + << "XL_NuXL:total_Morph" + << "XL_NuXL:total_HS"; +#endif + + feature_set + << "NuXL:marker_ions_score" + << "NuXL:partial_loss_score" << "NuXL:pl_MIC" << "NuXL:pl_err" << "NuXL:pl_Morph" << "NuXL:pl_modds" << "NuXL:pl_pc_MIC" - << "NuXL:pl_im_MIC" - << "NuXL:total_MIC" + << "NuXL:pl_im_MIC"; + + feature_set + << "NuXL:isPhospho" + << "NuXL:isXL" + << "NuXL:score" + << "isotope_error" + << "variable_modifications" + << "precursor_intensity_log10" << "NuXL:NA_MASS_z0" << "NuXL:NA_length" - << "NuXL:ladder_score" - << "NuXL:sequence_score" - << "NuXL:total_Morph" - << "NuXL:total_HS" - << "precursor_intensity_log10" << "nucleotide_mass_tags"; - if (!purities.empty()) feature_set << "precursor_purity"; - + if (!purities.empty()) feature_set << "precursor_purity"; // one-hot encoding of cross-linked nucleotide const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); for (const auto& c : can_cross_link) @@ -2895,11 +3021,75 @@ static void scoreShiftedFragments_( return count + MIC; // Morph score of matched (complete / partial) ladder } + String convertRawFile_(const String& in) + { + writeLog_("RawFileReader reading tool. Copyright 2016 by Thermo Fisher Scientific, Inc. All rights reserved"); + String net_executable = getStringOption_("NET_executable"); + TOPPBase::ExitCodes exit_code; + QStringList arguments; + String out = in + ".mzML"; + // check if this file exists and not empty so we can skip further conversions + if (!File::empty(out)) { return out; } +#ifdef OPENMS_WINDOWSPLATFORM + if (net_executable.empty()) + { // default on Windows: if no mono executable is set use the "native" .NET one + arguments << String("-i=" + in).toQString() + << String("--output_file=" + out).toQString() + << String("-f=2").toQString() // indexedMzML + << String("-e").toQString(); // ignore instrument errors + if (no_peak_picking) { arguments << String("--noPeakPicking").toQString(); } + exit_code = runExternalProcess_(getStringOption_("ThermoRaw_executable").toQString(), arguments); + } + else + { // use e.g., mono + arguments << getStringOption_("ThermoRaw_executable").toQString() + << String("-i=" + in).toQString() + << String("--output_file=" + out).toQString() + << String("-f=2").toQString() + << String("-e").toQString(); + if (no_peak_picking) { arguments << String("--noPeakPicking").toQString(); } + exit_code = runExternalProcess_(net_executable.toQString(), arguments); + } +#else + // default on Mac, Linux: use mono + net_executable = net_executable.empty() ? "mono" : net_executable; + arguments << getStringOption_("ThermoRaw_executable").toQString() + << String("-i=" + in).toQString() + << String("--output_file=" + out).toQString() + << String("-f=2").toQString() + << String("-e").toQString(); + exit_code = runExternalProcess_(net_executable.toQString(), arguments); +#endif + if (exit_code != ExitCodes::EXECUTION_OK) + { + OPENMS_LOG_ERROR << "File conversion from RAW file to mzML failed." << endl; + } + else + { + OPENMS_LOG_INFO << "Raw File successfuly converted to mzML." << endl; + OPENMS_LOG_INFO << "Please delete it if not needed anymore." << endl; + } + return out; + } + ExitCodes main_(int, const char**) override { ProgressLogger progresslogger; progresslogger.setLogType(log_type_); - String in_mzml = getStringOption_("in"); + + FileHandler fh; + FileTypes::Type in_type = fh.getType(getStringOption_("in")); + + String in_mzml; + if (in_type == FileTypes::MZML) + { + in_mzml = getStringOption_("in"); + } + else if (in_type == FileTypes::RAW) + { + in_mzml = convertRawFile_(getStringOption_("in")); + } + String in_db = getStringOption_("database"); String out_idxml = getStringOption_("out"); String out_csv = getStringOption_("out_tsv"); @@ -2953,6 +3143,8 @@ static void scoreShiftedFragments_( Size max_variable_mods_per_peptide = getIntOption_("modifications:variable_max_per_peptide"); size_t report_top_hits = (size_t)getIntOption_("report:top_hits"); + double peptide_FDR = getDoubleOption_("report:peptideFDR"); + double XL_FDR = getDoubleOption_("report:xlFDR"); // string format: target,formula e.g. "A=C10H14N5O7P", ..., "U=C10H14N5O7P", "X=C9H13N2O8PS" where X represents tU StringList target_nucleotides = getStringList_("RNPxl:target_nucleotides"); @@ -3678,10 +3870,127 @@ static void scoreShiftedFragments_( // annotate RNPxl related information to hits and create report vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); - if (generate_decoys) { fdr.apply(peptide_ids); } + if (generate_decoys) + { + fdr.apply(peptide_ids); + + // write ProteinIdentifications and PeptideIdentifications to IdXML + IdXMLFile().store(out_idxml, protein_ids, peptide_ids); + + // generate filtered results + IDFilter::keepNBestHits(peptide_ids, 1); - // write ProteinIdentifications and PeptideIdentifications to IdXML - IdXMLFile().store(out_idxml, protein_ids, peptide_ids); + // split PSMs into XLs and non-XLs but keep only best one of both + vector pep_pi; + vector xl_pi; + for (auto pi : peptide_ids) + { + vector pep_ph; + vector xl_ph; + for (auto ph : pi.getHits()) + { + if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) + { // only add best hit + if (pep_ph.empty() && xl_ph.empty()) pep_ph.push_back(ph); + } + else + { + if (pep_ph.empty() && xl_ph.empty()) xl_ph.push_back(ph); + } + } + if (!pep_ph.empty()) { pep_pi.push_back(pi); pep_pi.back().setHits(pep_ph); } + if (!xl_ph.empty()) { xl_pi.push_back(pi); xl_pi.back().setHits(xl_ph); } + } + + // calculate FDRs separately + fdr.apply(xl_pi); + fdr.apply(pep_pi); + + if (peptide_FDR > 0.0 && peptide_FDR < 1.0) + { + IDFilter::filterHitsByScore(pep_pi, peptide_FDR); + } + + if (XL_FDR > 0.0 && XL_FDR < 1.0) + { + IDFilter::filterHitsByScore(xl_pi, XL_FDR); + } + String out2(out_idxml); + out2.substitute(".idXML", "_"); + IdXMLFile().store(out2 + String::number(XL_FDR, 4) + "_XLs.idXML", protein_ids, xl_pi); + IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", protein_ids, pep_pi); + + String percolator_executable = getStringOption_("percolator_executable"); + if (!percolator_executable.empty()) + { + // run percolator on idXML + String perc_out = out_idxml; + perc_out.substitute(".idXML", "_perc.idXML"); + QStringList process_params; + process_params << "-percolator_executable" << percolator_executable.toQString() + << "-train_best_positive" + << "-score_type" << "svm" + << "-in" << out_idxml.toQString() + << "-out" << perc_out.toQString(); + TOPPBase::ExitCodes exit_code = runExternalProcess_(percolator_executable.toQString(), process_params); + if (exit_code != EXECUTION_OK) + { + OPENMS_LOG_WARN << "Score recalibration failed." << endl; + } + else + { + // load back idXML + IdXMLFile().load(perc_out, protein_ids, peptide_ids); + + // generate filtered results + IDFilter::keepNBestHits(peptide_ids, 1); + + // split PSMs into XLs and non-XLs but keep only best one of both + vector pep_pi; + vector xl_pi; + for (auto pi : peptide_ids) + { + vector pep_ph, xl_ph; + for (auto ph : pi.getHits()) + { + if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) + { // only add best hit + if (pep_ph.empty() && xl_ph.empty()) pep_ph.push_back(ph); + } + else + { + if (pep_ph.empty() && xl_ph.empty()) xl_ph.push_back(ph); + } + } + if (!pep_ph.empty()) { pep_pi.push_back(pi); pep_pi.back().setHits(pep_ph); } + if (!xl_ph.empty()) { xl_pi.push_back(pi); xl_pi.back().setHits(xl_ph); } + } + + // calculate FDRs separately + fdr.apply(xl_pi); + fdr.apply(pep_pi); + + if (peptide_FDR > 0.0 && peptide_FDR < 1.0) + { + IDFilter::filterHitsByScore(pep_pi, peptide_FDR); + } + + if (XL_FDR > 0.0 && XL_FDR < 1.0) + { + IDFilter::filterHitsByScore(xl_pi, XL_FDR); + } + String out2(out_idxml); + out2.substitute(".idXML", "_perc_"); + IdXMLFile().store(out2 + String::number(XL_FDR, 4) + "_XLs.idXML", protein_ids, xl_pi); + IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", protein_ids, pep_pi); + } + } + } + else // no decoys + { + // write ProteinIdentifications and PeptideIdentifications to IdXML + IdXMLFile().store(out_idxml, protein_ids, peptide_ids); + } // save report if (!out_csv.empty()) From 651e16753585246a7cd0be9a3da2e608e866c391 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 23 Jul 2019 12:32:07 +0200 Subject: [PATCH 067/471] fixed missing annotation of marker ions --- .../ANALYSIS/RNPXL/RNPxlParameterParsing.cpp | 11 +- src/utils/OpenNuXL.cpp | 124 ++++++++++++------ 2 files changed, 93 insertions(+), 42 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp index 12f82daee82..60c22c68205 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp @@ -229,9 +229,9 @@ RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringList fragment_ MS2AdductsOfSinglePrecursorAdduct RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, - const String &exp_pc_formula, - const RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, - const set &can_xl) + const String &exp_pc_formula, + const RNPxlParameterParsing::NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, + const set &can_xl) { OPENMS_LOG_DEBUG << "Generating fragment adducts for precursor adduct: '" << exp_pc_adduct << "'" << endl; @@ -309,7 +309,10 @@ RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, for (auto const & n2fa : nucleotide_to_fragment_adducts) { const char & nucleotide = n2fa.first; // the nucleotide without any associated loss - if (exp_pc_nucleotide_count.find(nucleotide) != exp_pc_nucleotide_count.end()) { marker_ion_set.insert(n2fa.second.begin(), n2fa.second.end()); } + if (exp_pc_nucleotide_count.find(nucleotide) != exp_pc_nucleotide_count.end()) + { + marker_ion_set.insert(n2fa.second.begin(), n2fa.second.end()); + } } std::move(std::begin(marker_ion_set), std::end(marker_ion_set), std::back_inserter(ret.marker_ions)); } diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 60c9b44e41c..9a3efb28386 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -107,7 +107,6 @@ using namespace OpenMS; using namespace OpenMS::Internal; using namespace std; - // stores which residues (known to give rise to immonium ions) are in the sequence struct ImmoniumIonsInPeptide { @@ -376,6 +375,8 @@ class OpenNuXL : static constexpr double MIN_HYPERSCORE = 0.1; // hit's with lower score than this will be neglected (usually 1 or 0 matches) static constexpr double MIN_TOTAL_LOSS_IONS = 1; // minimum number of matches to unshifted ions static constexpr double MIN_SHIFTED_IONS = 1; // minimum number of matches to shifted ions (applies to XLs only) + static constexpr Size IA_CHARGE_INDEX = 0; + static constexpr Size IA_TAG_INDEX = 1; protected: void registerOptionsAndFlags_() override @@ -1171,7 +1172,8 @@ class OpenNuXL : const double nucleotide_mass_tags/*, const double fraction_of_top50annotated*/) { - return + 1.0 * ah.total_loss_score; + return + 1.0 * ah.total_loss_score + 0.01 * ah.total_MIC + 0.01 * ah.mass_error_p + - 0.01 * ah.isotope_error - ah.err - ah.pl_err; /* double score = 2.52872532 +0.38318303 * nucleotide_mass_tags; @@ -1268,9 +1270,9 @@ static void scoreShiftedFragments_( auto const & r = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0]); + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX]); marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } @@ -1284,7 +1286,7 @@ static void scoreShiftedFragments_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], intensity_sum, matched_peaks, partial_loss_sub_score, @@ -1323,7 +1325,7 @@ static void scoreShiftedFragments_( vector mzs; vector charges; for (auto const& p : spec) { mzs.push_back(p.getMZ()); } - for (auto const& p : spec.getIntegerDataArrays()[0]) { charges.push_back(p); } + for (auto const& p : spec.getIntegerDataArrays()[IA_CHARGE_INDEX]) { charges.push_back(p); } Size match(0), in_mass_range(0); for (Size i = 0; i != mzs.size(); ++i) @@ -1359,8 +1361,8 @@ static void scoreShiftedFragments_( sort(idx.begin(), idx.end(), [&spec](size_t i1, size_t i2) { return spec[i1].getIntensity() > spec[i2].getIntensity(); }); - for (int rank : idx) spec.getIntegerDataArrays()[1].push_back(rank); - spec.getIntegerDataArrays()[1].setName("intensity_rank"); + for (int rank : idx) spec.getIntegerDataArrays()[IA_TAG_INDEX].push_back(rank); + spec.getIntegerDataArrays()[IA_TAG_INDEX].setName("intensity_rank"); } } @@ -1430,7 +1432,7 @@ static void scoreShiftedFragments_( { // set Unknown charge to z=1. Otherwise we get a lot of spurious matches // to highly charged fragments in the low m/z region - DataArrays::IntegerDataArray& ia = spec.getIntegerDataArrays()[0]; // charge array + DataArrays::IntegerDataArray& ia = spec.getIntegerDataArrays()[IA_CHARGE_INDEX]; // charge array for (int & z : ia) { if (z == 0) { z = 1; } } } #ifdef DEBUG_OpenNuXL @@ -1655,7 +1657,7 @@ static void scoreShiftedFragments_( RNPxlFragmentIonGenerator::addMS2MarkerIons( marker_ions, marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0], + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX], marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); const PeakSpectrum& exp_spectrum = exp[scan_index]; @@ -1810,7 +1812,7 @@ static void scoreShiftedFragments_( RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( unmodified_sequence, total_loss_spectrum, - total_loss_spectrum.getIntegerDataArrays()[0], + total_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], total_loss_spectrum.getStringDataArrays()[0]); total_loss_spectrum.sortByPosition(); // need to resort after adding special immonium ions @@ -1837,7 +1839,7 @@ static void scoreShiftedFragments_( RNPxlFragmentIonGenerator::addMS2MarkerIons( marker_ions, partial_loss_spectrum, - partial_loss_spectrum.getIntegerDataArrays()[0], + partial_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], partial_loss_spectrum.getStringDataArrays()[0]); partial_loss_spectrum.sortByPosition(); // need to resort after adding marker ions @@ -1867,12 +1869,12 @@ static void scoreShiftedFragments_( fragment_mass_tolerance_unit_ppm, total_loss_spectrum, exp_spectrum, - total_loss_spectrum.getIntegerDataArrays()[0], - exp_spectrum.getIntegerDataArrays()[0], + total_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], ppm_error_array); const PeakSpectrum::StringDataArray& total_loss_annotations = total_loss_spectrum.getStringDataArrays()[0]; - const PeakSpectrum::IntegerDataArray& total_loss_charges = total_loss_spectrum.getIntegerDataArrays()[0]; + const PeakSpectrum::IntegerDataArray& total_loss_charges = total_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX]; for (auto const & aligned : alignment) { @@ -1886,7 +1888,7 @@ static void scoreShiftedFragments_( const String& ion_name = total_loss_annotations[aligned.first]; const int charge = total_loss_charges[aligned.first]; - OPENMS_PRECONDITION(exp_spectrum.getIntegerDataArrays().back()[fragment_index] == charge, "Charges in alignment must match."); + OPENMS_PRECONDITION(exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX][fragment_index] == charge, "Charges in alignment must match."); // define which ion names are annotated if (ion_name[0] == 'y') @@ -2037,12 +2039,12 @@ static void scoreShiftedFragments_( fragment_mass_tolerance_unit_ppm, partial_loss_spectrum, exp_spectrum, - partial_loss_spectrum.getIntegerDataArrays()[0], - exp_spectrum.getIntegerDataArrays()[0], + partial_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], ppm_error_array); const PeakSpectrum::StringDataArray& partial_loss_annotations = partial_loss_spectrum.getStringDataArrays()[0]; - const PeakSpectrum::IntegerDataArray& partial_loss_charges = partial_loss_spectrum.getIntegerDataArrays()[0]; + const PeakSpectrum::IntegerDataArray& partial_loss_charges = partial_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX]; if (alignment.empty()) { @@ -2060,7 +2062,7 @@ static void scoreShiftedFragments_( const Peak1D & fragment = exp_spectrum[fragment_index]; const double & fragment_intensity = fragment.getIntensity(); // in percent (%) const double & fragment_mz = fragment.getMZ(); - const int & fragment_charge = exp_spectrum.getIntegerDataArrays().back()[fragment_index]; + const int & fragment_charge = exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX][fragment_index]; #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "fragment_mz:" << fragment_mz << " fragment_charge:" << fragment_charge << endl; #endif @@ -2614,7 +2616,42 @@ static void scoreShiftedFragments_( purities); } } + // hits have rank and are sorted by score + map sequence_is_topPSM; + map> sequence_charges; // of top PSM + map sequence_is_XL; + map sequence_is_peptide; + for (const auto & pid : peptide_ids) + { + if (pid.getHits().empty()) continue; + const auto & top_hit = pid.getHits()[0]; + const String& unmodified_sequence = top_hit.getSequence().toUnmodifiedString(); + ++sequence_is_topPSM[unmodified_sequence]; + sequence_charges[unmodified_sequence].insert(top_hit.getCharge()); + if (static_cast(top_hit.getMetaValue("NuXL:isXL")) == 1) + { + ++sequence_is_XL[unmodified_sequence]; + } + else + { + ++sequence_is_peptide[unmodified_sequence]; + } + } + for (auto & pid : peptide_ids) + { + for (auto & ph : pid.getHits()) + { + const String& unmodified_sequence = ph.getSequence().toUnmodifiedString(); + if (sequence_is_topPSM.find(unmodified_sequence) != sequence_is_topPSM.end()) + { + ph.setMetaValue("CountSequenceIsTop", sequence_is_topPSM[unmodified_sequence]); + ph.setMetaValue("CountSequenceCharges", sequence_charges[unmodified_sequence].size()); + ph.setMetaValue("CountSequenceIsXL", sequence_is_XL[unmodified_sequence]); + ph.setMetaValue("CountSequenceIsPeptide", sequence_is_peptide[unmodified_sequence]); + } + } + } // protein identifications (leave as is...) protein_ids = vector(1); protein_ids[0].setDateTime(DateTime::now()); @@ -2741,7 +2778,12 @@ static void scoreShiftedFragments_( << "precursor_intensity_log10" << "NuXL:NA_MASS_z0" << "NuXL:NA_length" - << "nucleotide_mass_tags"; + << "nucleotide_mass_tags" + << "CountSequenceIsTop" + << "CountSequenceCharges" + << "CountSequenceIsXL" + << "CountSequenceIsPeptide"; + if (!purities.empty()) feature_set << "precursor_purity"; // one-hot encoding of cross-linked nucleotide const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); @@ -2850,7 +2892,7 @@ static void scoreShiftedFragments_( scorePeptideIons_( exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], total_loss_template_z1_b_ions, total_loss_template_z1_y_ions, current_peptide_mass_without_NA, @@ -3465,7 +3507,7 @@ static void scoreShiftedFragments_( vector peak_matched(exp_spectrum.size(), false); scorePeptideIons_( exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], total_loss_template_z1_b_ions, total_loss_template_z1_y_ions, current_peptide_mass_without_NA, @@ -3568,13 +3610,13 @@ static void scoreShiftedFragments_( const vector& partial_loss_modification = nuc_2_adducts.second; PeakSpectrum marker_ions_sub_score_spectrum_z1; - // add shifted marker ions + // add shifted marker ions of charge 1 marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation RNPxlFragmentIonGenerator::addMS2MarkerIons( marker_ions, marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0], + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX], marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); // nucleotide is associated with certain NA-related fragment losses? @@ -3607,7 +3649,7 @@ static void scoreShiftedFragments_( scorePeptideIons_( exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], total_loss_template_z1_b_ions, total_loss_template_z1_y_ions, current_peptide_mass_without_NA, @@ -3927,12 +3969,18 @@ static void scoreShiftedFragments_( String perc_out = out_idxml; perc_out.substitute(".idXML", "_perc.idXML"); QStringList process_params; - process_params << "-percolator_executable" << percolator_executable.toQString() - << "-train_best_positive" + process_params << "-in" << out_idxml.toQString() + << "-out" << perc_out.toQString() + << "-percolator_executable" << percolator_executable.toQString() + << "-train-best-positive" << "-score_type" << "svm" - << "-in" << out_idxml.toQString() - << "-out" << perc_out.toQString(); - TOPPBase::ExitCodes exit_code = runExternalProcess_(percolator_executable.toQString(), process_params); + << "-post-processing-tdc" +#if DEBUG_OpenNuXL + << "-out_pout_target" << "merged_target.tab" << "-out_pout_decoy" << "merged_decoy.tab" +#endif + ; + TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); + if (exit_code != EXECUTION_OK) { OPENMS_LOG_WARN << "Score recalibration failed." << endl; @@ -4034,9 +4082,9 @@ static void scoreShiftedFragments_( auto const & r = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[0]); + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX]); marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } @@ -4051,17 +4099,17 @@ static void scoreShiftedFragments_( partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], *pl_spec, - pl_spec->getIntegerDataArrays()[0], + pl_spec->getIntegerDataArrays()[IA_CHARGE_INDEX], intensity_sum); auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[0], + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], *pl_spec, - pl_spec->getIntegerDataArrays()[0]); + pl_spec->getIntegerDataArrays()[IA_CHARGE_INDEX]); plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; plss_Morph = pl_sub_scores.score; From f7f824ae547a4ef18e463344eff2a94655c410d0 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 23 Jul 2019 14:39:39 +0200 Subject: [PATCH 068/471] filter protein ids --- src/utils/OpenNuXL.cpp | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 9a3efb28386..47d8a246d38 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -3921,6 +3921,7 @@ static void scoreShiftedFragments_( // generate filtered results IDFilter::keepNBestHits(peptide_ids, 1); + IDFilter::removeUnreferencedProteins(protein_ids, peptide_ids); // split PSMs into XLs and non-XLs but keep only best one of both vector pep_pi; @@ -3959,8 +3960,16 @@ static void scoreShiftedFragments_( } String out2(out_idxml); out2.substitute(".idXML", "_"); - IdXMLFile().store(out2 + String::number(XL_FDR, 4) + "_XLs.idXML", protein_ids, xl_pi); - IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", protein_ids, pep_pi); + { + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); + IdXMLFile().store(out2 + String::number(XL_FDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); + } + { + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, pep_pi); + IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", tmp_prots, pep_pi); + } String percolator_executable = getStringOption_("percolator_executable"); if (!percolator_executable.empty()) @@ -3992,6 +4001,7 @@ static void scoreShiftedFragments_( // generate filtered results IDFilter::keepNBestHits(peptide_ids, 1); + IDFilter::removeUnreferencedProteins(protein_ids, peptide_ids); // split PSMs into XLs and non-XLs but keep only best one of both vector pep_pi; @@ -4029,8 +4039,16 @@ static void scoreShiftedFragments_( } String out2(out_idxml); out2.substitute(".idXML", "_perc_"); - IdXMLFile().store(out2 + String::number(XL_FDR, 4) + "_XLs.idXML", protein_ids, xl_pi); - IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", protein_ids, pep_pi); + { + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); + IdXMLFile().store(out2 + String::number(XL_FDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); + } + { + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, pep_pi); + IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", tmp_prots, pep_pi); + } } } } From d9f8b9ca08d6aac0f5250a540fa4c69d7cf3821b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 26 Jul 2019 15:08:58 +0200 Subject: [PATCH 069/471] filter out bad PSMs that messed up results against large databases --- src/topp/PercolatorAdapter.cpp | 6 +++++ src/utils/OpenNuXL.cpp | 46 +++++++++++++++++++++++----------- 2 files changed, 38 insertions(+), 14 deletions(-) diff --git a/src/topp/PercolatorAdapter.cpp b/src/topp/PercolatorAdapter.cpp index 7baa085a91c..a9df2b29e57 100644 --- a/src/topp/PercolatorAdapter.cpp +++ b/src/topp/PercolatorAdapter.cpp @@ -328,6 +328,12 @@ class PercolatorAdapter : else if ((idx = it->find("index=")) != string::npos) { scan_number = it->substr(idx + 6).toInt(); + break; + } + else if ((idx = it->find("spectrum=")) != string::npos) + { + scan_number = it->substr(idx + 9).toInt(); + break; } } return scan_number; diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 47d8a246d38..9f4de3207c4 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -531,10 +531,19 @@ class OpenNuXL : { return (hyperScore < MIN_HYPERSCORE || tlss_Morph < MIN_TOTAL_LOSS_IONS + 1.0 -// || tlss_modds < 1e-10 || tlss_total_MIC < 0.01); } + static bool badPartialLossScore(float tlss_Morph, float plss_Morph, float plss_MIC, float plss_im_MIC, float plss_pc_MIC, float marker_ions_score) + { + if (plss_Morph + tlss_Morph < 5.03) return true; + + if (plss_MIC + plss_im_MIC + plss_pc_MIC + marker_ions_score < 0.01) return true; + + // if we don't see shifted ladder ions, we need at least some signal in the shifted immonium ions + return (plss_Morph < MIN_SHIFTED_IONS + 1.0 && plss_im_MIC < 0.01); + } + /* @param N number of theoretical peaks @param peak_in_spectrum number of experimental peaks @@ -1134,7 +1143,8 @@ class OpenNuXL : // according to A. Stuetzer mainly observed with C‘-NH3 (94.0167 Da) match_one_peak_z1(imK2 + fa.mass, plss_im_MIC); // usually only observed without shift (A. Stuetzer) - match_one_peak_z1(imK3 + fa.mass, plss_im_MIC); + // TODO: only enable for DNA? get's sometimes matched by chance + // match_one_peak_z1(imK3 + fa.mass, plss_im_MIC); } if (iip.M) { @@ -1172,8 +1182,11 @@ class OpenNuXL : const double nucleotide_mass_tags/*, const double fraction_of_top50annotated*/) { +/* Tie-braker score return + 1.0 * ah.total_loss_score + 0.01 * ah.total_MIC + 0.01 * ah.mass_error_p - 0.01 * ah.isotope_error - ah.err - ah.pl_err; +*/ + /* double score = 2.52872532 +0.38318303 * nucleotide_mass_tags; @@ -1213,7 +1226,6 @@ score += ah.mass_error_p * 1.15386068 //TODO: check Alex if (ah.Morph + ah.pl_Morph < 5.03) return 0; // return ah.total_MIC + ah.marker_ions_score + fraction_of_top50annotated; -/* return -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err + 52.2888 * ah.pl_err - 0.0105 * ah.modds @@ -1222,7 +1234,9 @@ score += ah.mass_error_p * 1.15386068 + 2.59655 * ah.total_MIC + 2.38320 * ah.ladder_score + 0.65422535 * (ah.total_loss_score + ah.partial_loss_score); // 4267 without perc / 5306 with perc auf 1- // 5010 with perc auf 2- -*/ + + + // return -7.9010278 + 0.7545435 * ah.total_loss_score + 3.1219378 * ah.sequence_score + 0.33 * ah.mass_error_p + 0.01*ah.total_MIC; } @@ -2779,10 +2793,13 @@ static void scoreShiftedFragments_( << "NuXL:NA_MASS_z0" << "NuXL:NA_length" << "nucleotide_mass_tags" +#ifdef DANGEROUS_FEAUTURES << "CountSequenceIsTop" << "CountSequenceCharges" << "CountSequenceIsXL" - << "CountSequenceIsPeptide"; + << "CountSequenceIsPeptide" +#endif + ; if (!purities.empty()) feature_set << "precursor_purity"; // one-hot encoding of cross-linked nucleotide @@ -3699,17 +3716,12 @@ static void scoreShiftedFragments_( plss_im_MIC); const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC + marker_ions_sub_score; - -/* - // less then two shifted peaks? seems to throw out some good hits ??? - if ( partial_loss_sub_score < MIN_HYPERSCORE // at least one peak with 10% of max intensity - || plss_Morph < MIN_SHIFTED_IONS + 1.0 // > 1 shifted peaks - || total_MIC < 0.01 // less than 1% explained peaks - ) + + if (badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, plss_pc_MIC, marker_ions_sub_score)) { continue; } -*/ + const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; @@ -3948,7 +3960,10 @@ static void scoreShiftedFragments_( // calculate FDRs separately fdr.apply(xl_pi); fdr.apply(pep_pi); - + + IDFilter::removeDecoyHits(xl_pi); + IDFilter::removeDecoyHits(pep_pi); + if (peptide_FDR > 0.0 && peptide_FDR < 1.0) { IDFilter::filterHitsByScore(pep_pi, peptide_FDR); @@ -4027,6 +4042,9 @@ static void scoreShiftedFragments_( // calculate FDRs separately fdr.apply(xl_pi); fdr.apply(pep_pi); + + IDFilter::removeDecoyHits(xl_pi); + IDFilter::removeDecoyHits(pep_pi); if (peptide_FDR > 0.0 && peptide_FDR < 1.0) { From 5327932455eed244ef131059cfc8e84fcf087247 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Sun, 28 Jul 2019 14:11:30 +0200 Subject: [PATCH 070/471] nop --- src/utils/OpenNuXL.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 9f4de3207c4..a533a9773c5 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -1182,10 +1182,9 @@ class OpenNuXL : const double nucleotide_mass_tags/*, const double fraction_of_top50annotated*/) { -/* Tie-braker score - return + 1.0 * ah.total_loss_score + 0.01 * ah.total_MIC + 0.01 * ah.mass_error_p - - 0.01 * ah.isotope_error - ah.err - ah.pl_err; -*/ +// Tie-braker score +// return + 1.0 * ah.total_loss_score + ah.total_MIC + 0.1 * ah.mass_error_p +// - 0.01 * ah.isotope_error - 10.0 * ah.err - 10.0 * ah.pl_err; /* double score = 2.52872532 @@ -1232,6 +1231,7 @@ score += ah.mass_error_p * 1.15386068 + 88.7997 * ah.immonium_score- 0.88823 * ah.partial_loss_score + 14.2052 * ah.pl_MIC + 0.61144 * ah.pl_modds + 10.07574543 * ah.pl_pc_MIC -28.05701 * ah.pl_im_MIC + 2.59655 * ah.total_MIC + 2.38320 * ah.ladder_score + 0.65422535 * (ah.total_loss_score + ah.partial_loss_score); + // 4267 without perc / 5306 with perc auf 1- // 5010 with perc auf 2- From 06ad6e958467ca0d878f6d0e8269b50f853cb773 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 29 Jul 2019 17:02:41 +0200 Subject: [PATCH 071/471] twice marker ion tolerance --- src/utils/OpenNuXL.cpp | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index a533a9773c5..022d997adf4 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -538,10 +538,10 @@ class OpenNuXL : { if (plss_Morph + tlss_Morph < 5.03) return true; - if (plss_MIC + plss_im_MIC + plss_pc_MIC + marker_ions_score < 0.01) return true; + if (plss_MIC + plss_im_MIC + plss_pc_MIC + marker_ions_score < 0.03) return true; // if we don't see shifted ladder ions, we need at least some signal in the shifted immonium ions - return (plss_Morph < MIN_SHIFTED_IONS + 1.0 && plss_im_MIC < 0.01); + return (plss_Morph < MIN_SHIFTED_IONS + 1.0 && plss_im_MIC < 0.03); } /* @@ -1226,15 +1226,23 @@ score += ah.mass_error_p * 1.15386068 // return ah.total_MIC + ah.marker_ions_score + fraction_of_top50annotated; return - -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err + 10.0 * ah.total_loss_score + ah.partial_loss_score + + 0.01 * ah.mass_error_p + - 10.0 * ah.err + - 10.0 * ah.pl_err + + 3.0 * ah.pl_MIC + + isXL * 3.0 * ah.marker_ions_score + + 3.0 * ah.total_MIC + ah.ladder_score; + +/* + -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err + 52.2888 * ah.pl_err - 0.0105 * ah.modds + 88.7997 * ah.immonium_score- 0.88823 * ah.partial_loss_score + 14.2052 * ah.pl_MIC + 0.61144 * ah.pl_modds + 10.07574543 * ah.pl_pc_MIC -28.05701 * ah.pl_im_MIC - + 2.59655 * ah.total_MIC + 2.38320 * ah.ladder_score + 0.65422535 * (ah.total_loss_score + ah.partial_loss_score); - + + 2.59655 * ah.total_MIC + 2.38320 * ah.ladder_score + 0.65422535 * (ah.total_loss_score + ah.partial_loss_score) // 4267 without perc / 5306 with perc auf 1- // 5010 with perc auf 2- - +*/ @@ -1249,7 +1257,7 @@ score += ah.mass_error_p * 1.15386068 + 0.333 * ah.mass_error_p*/; } /* -* Score fragments carrying NA adducts . +* Score fragments carrying NA adducts */ static void scoreShiftedFragments_( const vector &partial_loss_modification, @@ -1281,7 +1289,7 @@ static void scoreShiftedFragments_( if (!marker_ions_sub_score_spectrum_z1.empty()) { - auto const & r = MorpheusScore::compute(fragment_mass_tolerance, + auto const & r = MorpheusScore::compute(fragment_mass_tolerance * 2.0, fragment_mass_tolerance_unit_ppm, exp_spectrum, exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], @@ -3899,7 +3907,6 @@ static void scoreShiftedFragments_( param_pi.setValue("enzyme:name", getStringOption_("peptide:enzyme")); param_pi.setValue("enzyme:specificity", "full"); param_pi.setValue("missing_decoy_action", "silent"); - param_pi.setValue("log", getStringOption_("log")); indexer.setParameters(param_pi); PeptideIndexing::ExitCodes indexer_exit = indexer.run(fasta_db, protein_ids, peptide_ids); From 89ca699d144ffe6d49e1a044a127a7ab497233ce Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 30 Jul 2019 09:47:17 +0200 Subject: [PATCH 072/471] some style fixes --- src/utils/OpenNuXL.cpp | 33 ++++++++++++++++++--------------- 1 file changed, 18 insertions(+), 15 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 022d997adf4..2ec7e665c12 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -1179,8 +1179,9 @@ class OpenNuXL : */ static float calculateCombinedScore(const AnnotatedHit& ah, const bool isXL, - const double nucleotide_mass_tags/*, - const double fraction_of_top50annotated*/) + const double nucleotide_mass_tags + //, const double fraction_of_top50annotated + ) { // Tie-braker score // return + 1.0 * ah.total_loss_score + ah.total_MIC + 0.1 * ah.mass_error_p @@ -1240,8 +1241,8 @@ score += ah.mass_error_p * 1.15386068 + 88.7997 * ah.immonium_score- 0.88823 * ah.partial_loss_score + 14.2052 * ah.pl_MIC + 0.61144 * ah.pl_modds + 10.07574543 * ah.pl_pc_MIC -28.05701 * ah.pl_im_MIC + 2.59655 * ah.total_MIC + 2.38320 * ah.ladder_score + 0.65422535 * (ah.total_loss_score + ah.partial_loss_score) -// 4267 without perc / 5306 with perc auf 1- -// 5010 with perc auf 2- + 4267 without perc / 5306 with perc auf 1- + 5010 with perc auf 2- */ @@ -2800,16 +2801,17 @@ static void scoreShiftedFragments_( << "precursor_intensity_log10" << "NuXL:NA_MASS_z0" << "NuXL:NA_length" - << "nucleotide_mass_tags" + << "nucleotide_mass_tags"; #ifdef DANGEROUS_FEAUTURES + feature_set << "CountSequenceIsTop" << "CountSequenceCharges" << "CountSequenceIsXL" - << "CountSequenceIsPeptide" + << "CountSequenceIsPeptide"; #endif - ; + + if (!purities.empty()) feature_set << "precursor_purity"; - if (!purities.empty()) feature_set << "precursor_purity"; // one-hot encoding of cross-linked nucleotide const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); for (const auto& c : can_cross_link) @@ -3088,7 +3090,7 @@ static void scoreShiftedFragments_( return count + MIC; // Morph score of matched (complete / partial) ladder } - String convertRawFile_(const String& in) + String convertRawFile_(const String& in, bool no_peak_picking = false) { writeLog_("RawFileReader reading tool. Copyright 2016 by Thermo Fisher Scientific, Inc. All rights reserved"); String net_executable = getStringOption_("NET_executable"); @@ -3125,6 +3127,7 @@ static void scoreShiftedFragments_( << String("--output_file=" + out).toQString() << String("-f=2").toQString() << String("-e").toQString(); + if (no_peak_picking) { arguments << String("--noPeakPicking").toQString(); } exit_code = runExternalProcess_(net_executable.toQString(), arguments); #endif if (exit_code != ExitCodes::EXECUTION_OK) @@ -3945,11 +3948,11 @@ static void scoreShiftedFragments_( // split PSMs into XLs and non-XLs but keep only best one of both vector pep_pi; vector xl_pi; - for (auto pi : peptide_ids) + for (const auto & pi : peptide_ids) { vector pep_ph; vector xl_ph; - for (auto ph : pi.getHits()) + for (const auto & ph : pi.getHits()) { if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) { // only add best hit @@ -4005,9 +4008,9 @@ static void scoreShiftedFragments_( << "-percolator_executable" << percolator_executable.toQString() << "-train-best-positive" << "-score_type" << "svm" - << "-post-processing-tdc" + << "-post-processing-tdc"; #if DEBUG_OpenNuXL - << "-out_pout_target" << "merged_target.tab" << "-out_pout_decoy" << "merged_decoy.tab" + process_params << "-out_pout_target" << "merged_target.tab" << "-out_pout_decoy" << "merged_decoy.tab"; #endif ; TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); @@ -4028,10 +4031,10 @@ static void scoreShiftedFragments_( // split PSMs into XLs and non-XLs but keep only best one of both vector pep_pi; vector xl_pi; - for (auto pi : peptide_ids) + for (const auto & pi : peptide_ids) { vector pep_ph, xl_ph; - for (auto ph : pi.getHits()) + for (const auto & ph : pi.getHits()) { if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) { // only add best hit From 7be98a86ed68b97b2c030c79693156874c8b2500 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 14 Aug 2019 16:38:41 +0200 Subject: [PATCH 073/471] rank product of intensities, mass tags spanning modification, mass error calculations --- src/utils/OpenNuXL.cpp | 410 ++++++++++++++++++++++++++++++++++++++--- 1 file changed, 382 insertions(+), 28 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 2ec7e665c12..4a98cbec5df 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -337,6 +337,12 @@ class AnnotatedHit String best_localization; std::vector fragment_annotations; + size_t tag_unshifted = 0; + size_t tag_shifted = 0; + size_t tag_XLed = 0; // tag that contains the transition from unshifted to shifted + + double rank_product = 0; + static bool hasBetterScore(const AnnotatedHit& a, const AnnotatedHit& b) { return a.score > b.score; @@ -376,7 +382,7 @@ class OpenNuXL : static constexpr double MIN_TOTAL_LOSS_IONS = 1; // minimum number of matches to unshifted ions static constexpr double MIN_SHIFTED_IONS = 1; // minimum number of matches to shifted ions (applies to XLs only) static constexpr Size IA_CHARGE_INDEX = 0; - static constexpr Size IA_TAG_INDEX = 1; + static constexpr Size IA_RANK_INDEX = 1; protected: void registerOptionsAndFlags_() override @@ -1327,6 +1333,106 @@ static void scoreShiftedFragments_( if (plss_err > ft_da) plss_err = ft_da; } + class OPENMS_DLLAPI OpenNuXLTagger + { + public: + // initalize tagger with minimum/maximum tag length and +- tolerance ppm + OpenNuXLTagger(float ppm, size_t min_tag_length = 3, size_t max_tag_length = 65535) + { + ppm_ = ppm; + min_tag_length_ = min_tag_length; + max_tag_length_ = max_tag_length; + const std::set aas = ResidueDB::getInstance()->getResidues(); + for (const auto& r : aas) + { + const char letter = r->getOneLetterCode()[0]; + const float mass = r->getMonoWeight(Residue::Internal); + mass2aa[mass] = letter; + //cout << "Mass: " << mass << "\t" << letter << endl; + } + min_gap_ = mass2aa.begin()->first - Math::ppmToMass(ppm, mass2aa.begin()->first); + max_gap_ = mass2aa.rbegin()->first + Math::ppmToMass(ppm, mass2aa.rbegin()->first); + } + + void getTag(const std::vector& mzs, std::set& tags) const + { + // start peak + std::string tag; + if (min_tag_length_ > mzs.size()) return; // avoid segfault + + for (size_t i = 0; i < mzs.size() - min_tag_length_; ++i) + { + getTag_(tag, mzs, i, tags); + tag.clear(); + } + } + + // generate tags from mass vector @mzs using the standard residues in ResidueDB + void getTag(const MSSpectrum& spec, std::set& tags) const + { + const size_t N = spec.size(); + if (N < min_tag_length_) { return; } + // copy to float vector (speed) + std::vector mzs; + mzs.reserve(N); + for (auto const& p : spec) { mzs.push_back(p.getMZ()); } + getTag(mzs, tags); + } + + private: + float min_gap_; // will be set to smallest residue mass in ResidueDB + float max_gap_; // will be set to highest residue mass in ResidueDB + float ppm_; // < tolerance + size_t min_tag_length_; // < minimum tag length + size_t max_tag_length_; // < maximum tag length + std::map mass2aa; + char getAAByMass_(float m) const + { + // fast check for border cases + if (m < min_gap_ || m > max_gap_) return ' '; + const float delta = Math::ppmToMass(ppm_, m); + auto left = mass2aa.lower_bound(m - delta); + //if (left == mass2aa.end()) return ' '; // cannot happen, since we checked boundaries above + if (fabs(left->second - m) < delta) return left->second; + return ' '; + } + + void getTag_(std::string & tag, const std::vector& mzs, const size_t i, std::set& tags) const + { + const size_t N = mzs.size(); + size_t j = i + 1; + // recurse for all peaks in distance < max_gap + while (j < N) + { + if (tag.size() == max_tag_length_) { return; } // maximum tag size reached? - continue with next parent + + const float gap = mzs[j] - mzs[i]; + //cout << i << "\t" << j << "\t" << mzs[i] << "\t" << mzs[j] << "\t" << gap << endl; + if (gap > max_gap_) { return; } // already too far away - continue with next parent + const char aa = getAAByMass_(gap); + if (aa == ' ') { ++j; continue; } // can't extend tag + tag += aa; + getTag_(tag, mzs, j, tags); + if (tag.size() >= min_tag_length_) tags.insert(tag); + tag.pop_back(); // remove last char + ++j; + } + } + }; + + + double rankProduct_(const MSSpectrum& spectrum, vector peak_matched) + { + double rp(0); + for (size_t i = 0; i != peak_matched.size(); ++i) + { + if (!peak_matched[i]) continue; + const double rank = 1 + spectrum.getIntegerDataArrays()[IA_RANK_INDEX][i]; // ranks start at 0 -> add 1 + rp += 1.0/(double)peak_matched.size() * log((double)rank); + } + return exp(rp); + } + void calculateNucleotideTags_(PeakMap& exp, const double fragment_mass_tolerance, const bool fragment_mass_tolerance_unit_ppm, @@ -1341,6 +1447,31 @@ static void scoreShiftedFragments_( adduct_mass.insert(fa.mass); } } + + // mass shift to residue + adduct (including no adduct) + map > aa_plus_adduct_mass; + auto residues = ResidueDB::getInstance()->getResidues("Natural20"); + + for (const double d : adduct_mass) + { + for (const Residue* r : residues) + { + double m = d + r->getMonoWeight(Residue::Internal); + if (aa_plus_adduct_mass.count(m) > 0) cout << "WARNING: mass " << m << " of residue " << r->getName() << " with adduct " << d << " already present." << endl; + aa_plus_adduct_mass[m] = {r, d}; + } + } + // add mass shits of plain residues + for (const Residue* r : residues) + { + double m = r->getMonoWeight(Residue::Internal); + if (aa_plus_adduct_mass.count(m) > 0) cout << "WARNING: mass " << m << " of residue " << r->getName() << " already present." << endl; + aa_plus_adduct_mass[m] = {r, 0}; + } + + map adduct_mass_count; + map aa_plus_adduct_mass_count; + for (auto & spec : exp) { if (spec.getMSLevel() != 2) continue; @@ -1350,7 +1481,8 @@ static void scoreShiftedFragments_( for (auto const& p : spec) { mzs.push_back(p.getMZ()); } for (auto const& p : spec.getIntegerDataArrays()[IA_CHARGE_INDEX]) { charges.push_back(p); } - Size match(0), in_mass_range(0); + size_t match(0); + size_t in_mass_range(0); for (Size i = 0; i != mzs.size(); ++i) { for (Size j = i+1; j < mzs.size(); ++j) @@ -1361,10 +1493,37 @@ static void scoreShiftedFragments_( if (charges[i] != charges[j]) continue; const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, m) : fragment_mass_tolerance; - auto left = adduct_mass.lower_bound((dm*charges[i]) - tolerance); + auto left = adduct_mass.lower_bound((dm * charges[i]) - tolerance); if (left == adduct_mass.end()) continue; ++in_mass_range; - if (fabs(*left - (dm*charges[i])) < tolerance ) ++match; + if (fabs(*left - (dm * charges[i])) < tolerance ) + { + ++match; + ++adduct_mass_count[*left]; + } + } + } + + size_t aa_plus_adduct_match(0); + size_t aa_plus_adduct_in_mass_range(0); + for (Size i = 0; i != mzs.size(); ++i) + { + for (Size j = i+1; j < mzs.size(); ++j) + { + double m = mzs[j]; + double dm = m - mzs[i]; + + if (charges[i] != charges[j]) continue; + + const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, m) : fragment_mass_tolerance; + auto left = aa_plus_adduct_mass.lower_bound((dm * charges[i]) - tolerance); + if (left == aa_plus_adduct_mass.end()) continue; + ++aa_plus_adduct_in_mass_range; + if (fabs(left->first - (dm * charges[i])) < tolerance ) + { + ++aa_plus_adduct_match; + ++aa_plus_adduct_mass_count[left->first]; + } } } @@ -1372,7 +1531,6 @@ static void scoreShiftedFragments_( spec.getFloatDataArrays()[1].push_back((double)match / (double)in_mass_range); spec.getFloatDataArrays()[1].setName("nucleotide_mass_tags"); - spec.getIntegerDataArrays().resize(2); // calculate ranks // @@ -1384,10 +1542,51 @@ static void scoreShiftedFragments_( sort(idx.begin(), idx.end(), [&spec](size_t i1, size_t i2) { return spec[i1].getIntensity() > spec[i2].getIntensity(); }); - for (int rank : idx) spec.getIntegerDataArrays()[IA_TAG_INDEX].push_back(rank); - spec.getIntegerDataArrays()[IA_TAG_INDEX].setName("intensity_rank"); - + for (int rank : idx) spec.getIntegerDataArrays()[IA_RANK_INDEX].push_back(rank); + spec.getIntegerDataArrays()[IA_RANK_INDEX].setName("intensity_rank"); + } +/* + for (const auto& mra : aa_plus_adduct_mass) + { + double m = mra.first; + const pair& residue_adduct = mra.second; + cout << m << "\t" << residue_adduct.first->getOneLetterCode() << "\ŧ" << residue_adduct.second << endl; + } +*/ + + +/* + cout << "Distinct residue + adduct pairs: " << aa_plus_adduct_mass_count.size() << endl; + map > aa2mass2count; + + for (const auto& mc : aa_plus_adduct_mass_count) + { + auto it = aa_plus_adduct_mass.lower_bound(mc.first - 1e-6); + if (it == aa_plus_adduct_mass.end()) continue; + const Residue* residue = it->second.first; + String name = residue->getName(); + aa2mass2count[residue][mc.first] = mc.second; } + cout << "Total counts per residue:" << endl; + for (const auto& aa2 : aa2mass2count) + { + for (const auto m2c : aa2.second) + { + cout << aa2.first->getName() << "\t" << m2c.first << "\t" << m2c.second << endl; // aa mass count + } + } + cout << "Normalized counts per residue:" << endl; + for (const auto& aa2 : aa2mass2count) + { + auto& mass2count = aa2.second; + for (const auto m2c : mass2count) + { + // normalize by counts + cout << aa2.first->getName() << "\t" << m2c.first << "\t" << (double)m2c.second / mass2count.begin()->second << endl ; // aa mass count + } + } +*/ + } /* @brief Filter spectra to remove noise. @@ -2414,7 +2613,8 @@ static void scoreShiftedFragments_( const Size max_variable_mods_per_peptide, const Size scan_index, const MSSpectrum& spec, - const vector& purities) + const vector& purities, + const vector& nr_candidates) { pi.setMetaValue("scan_index", static_cast(scan_index)); pi.setMetaValue("spectrum_reference", spec.getNativeID()); @@ -2497,6 +2697,10 @@ static void scoreShiftedFragments_( ph.setMetaValue(String("NuXL:pl_im_MIC"), ah.pl_im_MIC); ph.setMetaValue(String("NuXL:total_Morph"), ah.Morph + ah.pl_Morph); ph.setMetaValue(String("NuXL:total_HS"), ah.total_loss_score + ah.partial_loss_score); + + ph.setMetaValue(String("NuXL:tag_XLed"), ah.tag_XLed); + ph.setMetaValue(String("NuXL:tag_unshifted"), ah.tag_unshifted); + ph.setMetaValue(String("NuXL:tag_shifted"), ah.tag_shifted); ph.setMetaValue(String("NuXL:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses @@ -2561,6 +2765,8 @@ static void scoreShiftedFragments_( } ph.setMetaValue("nucleotide_mass_tags", (double)spec.getFloatDataArrays()[1][0]); + ph.setMetaValue("nr_candidates", nr_candidates[scan_index]); + ph.setMetaValue("NuXL:rank_product", ah.rank_product); ph.setPeakAnnotations(ah.fragment_annotations); ph.setMetaValue("isotope_error", static_cast(ah.isotope_error)); @@ -2595,7 +2801,8 @@ static void scoreShiftedFragments_( const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, Size max_variable_mods_per_peptide, - const vector& purities) + const vector& purities, + const vector& nr_candidates) { assert(annotated_XL_hits.size() == annotated_peptide_hits.size()); SignedSize hit_count = static_cast(annotated_XL_hits.size()); @@ -2622,7 +2829,8 @@ static void scoreShiftedFragments_( max_variable_mods_per_peptide, scan_index, spec, - purities); + purities, + nr_candidates); } if (!ahs_peptide.empty()) @@ -2636,7 +2844,8 @@ static void scoreShiftedFragments_( max_variable_mods_per_peptide, scan_index, spec, - purities); + purities, + nr_candidates); } } // hits have rank and are sorted by score @@ -2710,8 +2919,12 @@ static void scoreShiftedFragments_( << "NuXL:ladder_score" << "NuXL:sequence_score" << "NuXL:total_Morph" - << "NuXL:total_HS"; - + << "NuXL:total_HS" + << "NuXL:tag_XLed" + << "NuXL:tag_unshifted" + << "NuXL:tag_shifted" + << "nr_candidates" + << "NuXL:rank_product"; #ifdef OPENNUXL_SEPARATE_FEATURES for (auto & pi : peptide_ids) { @@ -3142,6 +3355,58 @@ static void scoreShiftedFragments_( return out; } + // datastructure to store longest tag in unshifte/shifted sequence and tag spanning the XL position + struct XLTags + { + size_t tag_unshifted = 0; + size_t tag_shifted = 0; + size_t tag_XLed = 0; // tag that contains the transition from unshifted to shifted + }; + + XLTags getLongestTagWithShift(const vector& intL, const vector& intXL) + { + // calculate longest consecutive unshifted / shifted sequence and longest sequence spanning unshifted + shifted residues + // Note to myself: kind of nice and simple algorithm by the way ;) + XLTags tags; + vector runL(intL.size(), 0); + size_t run(0); + for (int l = 0; l != intL.size(); ++l) + { + if (intL[l] == 0) { run = 0; continue; } + ++run; + runL[l] = run; + if (run > tags.tag_unshifted) tags.tag_unshifted = run; + } + + // runL[i] now contains current run length e.g.: 000123400100 + if (!intXL.empty()) + { + vector runX(intXL.size(), 0); + run = 0; + for (int x = (int)intXL.size() - 1; x >= 0; --x) // note the reverse order + { + if (intXL[x] == 0) { run = 0; continue; } + ++run; + runX[x] = run; + if (run > tags.tag_shifted) tags.tag_shifted = run; + } + // runX[i] now contains the longest run in X starting at position i e.g.: 00003210000 + + //vector runLX(intX.size(), 0); + size_t maximum_tag_length(0); + // calculate maximum tag that spans linear intensities and at least one XLed amino acid + for (Size i = 0; i < intXL.size() - 1; ++i) + { + if (runX[i + 1] == 0 || runL[i] == 0) continue; // must have one cross-linked amino acid next to non-cross-linked amino acid + const size_t tag_length = runL[i] + runX[i + 1]; // tag length if cross-link is introduced at amino acid i+1 + if (tag_length > maximum_tag_length) maximum_tag_length = tag_length; + } + tags.tag_XLed = maximum_tag_length; + } + return tags; + } + + ExitCodes main_(int, const char**) override { ProgressLogger progresslogger; @@ -3325,9 +3590,8 @@ static void scoreShiftedFragments_( spectra, multimap_mass_2_scan_index); - - // preallocate storage for PSMs + vector nr_candidates(spectra.size(), 0); vector > annotated_XLs(spectra.size(), vector()); for (auto & a : annotated_XLs) { a.reserve(2 * report_top_hits); } vector > annotated_peptides(spectra.size(), vector()); @@ -3497,6 +3761,7 @@ static void scoreShiftedFragments_( if (low_it == up_it) { continue; } // no matching precursor in data + // add peaks for b- and y- ions with charge 1 (sorted by m/z) // total / complete loss spectra are generated for fast and (slow) full scoring if (total_loss_template_z1_b_ions.empty()) // only create complete loss spectrum once as this is rather costly and need only to be done once per petide @@ -3517,8 +3782,16 @@ static void scoreShiftedFragments_( // score peptide without NA (same method as fast scoring) for (auto & l = low_it; l != up_it; ++l) { - //const double exp_pc_mass = l->first; const Size & scan_index = l->second.first; + // count candidate for spectrum +#ifdef _OPENMP + omp_set_lock(&(annotated_peptides_lock[scan_index])); + omp_set_lock(&(annotated_XLs_lock[scan_index])); + ++nr_candidates[scan_index]; + omp_unset_lock(&(annotated_XLs_lock[scan_index])); + omp_unset_lock(&(annotated_peptides_lock[scan_index])); +#endif + //const double exp_pc_mass = l->first; const int & isotope_error = l->second.second; const PeakSpectrum & exp_spectrum = spectra[scan_index]; const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); @@ -3551,7 +3824,7 @@ static void scoreShiftedFragments_( tlss_modds, tlss_err, pc_MIC, - im_MIC + im_MIC ); const double tlss_total_MIC = tlss_MIC + im_MIC + pc_MIC; @@ -3586,6 +3859,18 @@ static void scoreShiftedFragments_( ah.sequence_score = ladderScore_(range) / (double)intensity_sum.size(); } + ah.rank_product = rankProduct_(exp_spectrum, peak_matched); + + const XLTags longest_tags = getLongestTagWithShift(intensity_sum, vector()); + + // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one + if (longest_tags.tag_XLed == 0) continue; + + ah.tag_XLed = longest_tags.tag_XLed; + ah.tag_unshifted = longest_tags.tag_unshifted; + ah.tag_shifted = longest_tags.tag_shifted; + + // combined score const double tags = exp_spectrum.getFloatDataArrays()[1][0]; ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); @@ -3658,6 +3943,14 @@ static void scoreShiftedFragments_( for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; + // count candidate for spectrum +#ifdef _OPENMP + omp_set_lock(&(annotated_peptides_lock[scan_index])); + omp_set_lock(&(annotated_XLs_lock[scan_index])); + ++nr_candidates[scan_index]; + omp_unset_lock(&(annotated_XLs_lock[scan_index])); + omp_unset_lock(&(annotated_peptides_lock[scan_index])); +#endif const int & isotope_error = l->second.second; const PeakSpectrum & exp_spectrum = spectra[scan_index]; float tlss_MIC(0), @@ -3672,7 +3965,7 @@ static void scoreShiftedFragments_( const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); - vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); vector peak_matched(exp_spectrum.size(), false); scorePeptideIons_( @@ -3685,7 +3978,7 @@ static void scoreShiftedFragments_( iip, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - intensity_sum, + intensity_linear, peak_matched, hyperScore, tlss_MIC, @@ -3699,6 +3992,8 @@ static void scoreShiftedFragments_( const double tlss_total_MIC = tlss_MIC + im_MIC + pc_MIC; if (badTotalLossScore(hyperScore, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } + vector intensity_xls(total_loss_template_z1_b_ions.size(), 0.0); + float plss_MIC(0), plss_err(1.0), plss_Morph(0), @@ -3715,7 +4010,7 @@ static void scoreShiftedFragments_( partial_loss_template_z1_bions, partial_loss_template_z1_yions, marker_ions_sub_score_spectrum_z1, - intensity_sum, + intensity_xls, peak_matched, partial_loss_sub_score, marker_ions_sub_score, @@ -3727,7 +4022,8 @@ static void scoreShiftedFragments_( plss_im_MIC); const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC + marker_ions_sub_score; - + + // decreases number of hits (especially difficult cases - but also number of false discoveries) if (badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, plss_pc_MIC, marker_ions_sub_score)) { continue; @@ -3764,14 +4060,25 @@ static void scoreShiftedFragments_( ah.rna_mod_index = rna_mod_index; ah.isotope_error = isotope_error; - auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); - ah.ladder_score = ladderScore_(range) / (double)intensity_sum.size(); - range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); + auto range = make_pair(intensity_linear.begin(), intensity_linear.end()); + ah.ladder_score = ladderScore_(range) / (double)intensity_linear.size(); + range = longestCompleteLadder_(intensity_linear.begin(), intensity_linear.end()); if (range.second != range.first) { - ah.sequence_score = ladderScore_(range) / (double)intensity_sum.size(); + ah.sequence_score = ladderScore_(range) / (double)intensity_linear.size(); } + const XLTags longest_tags = getLongestTagWithShift(intensity_linear, intensity_xls); + + ah.rank_product = rankProduct_(exp_spectrum, peak_matched); + + ah.tag_XLed = longest_tags.tag_XLed; + ah.tag_unshifted = longest_tags.tag_unshifted; + ah.tag_shifted = longest_tags.tag_shifted; + + // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one + if (longest_tags.tag_XLed == 0) continue; + // combined score const double tags = exp_spectrum.getFloatDataArrays()[1][0]; ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); @@ -3805,6 +4112,13 @@ static void scoreShiftedFragments_( for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; +#ifdef _OPENMP + omp_set_lock(&(annotated_peptides_lock[scan_index])); + omp_set_lock(&(annotated_XLs_lock[scan_index])); + ++nr_candidates[scan_index]; + omp_unset_lock(&(annotated_XLs_lock[scan_index])); + omp_unset_lock(&(annotated_peptides_lock[scan_index])); +#endif const int & isotope_error = l->second.second; const double & exp_pc_mass = l->first; @@ -3900,7 +4214,8 @@ static void scoreShiftedFragments_( fixed_modifications, variable_modifications, max_variable_mods_per_peptide, - purities); + purities, + nr_candidates); progresslogger.endProgress(); // reindex ids @@ -3934,6 +4249,40 @@ static void scoreShiftedFragments_( // annotate RNPxl related information to hits and create report vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); + // determine average mass error / sd (needs to be after annotate for now) + map> map_index2ppm; + for (size_t index = 0; index != peptide_ids.size(); ++index) + { + if (peptide_ids[index].getHits().empty()) continue; + if (peptide_ids[index].getHits()[0].getMetaValue("target_decoy") == "target") + { + double ppm_error = peptide_ids[index].getHits()[0].getMetaValue(OpenMS::Constants::PRECURSOR_ERROR_PPM_USERPARAM); + map_index2ppm[peptide_ids[index].getHits()[0].getScore()] = ppm_error; + } + } + + size_t i(0); + double mean(0); + for (auto & m : map_index2ppm) + { + mean += m.second; + ++i; + if (peptide_ids.size() > 1000 && i > peptide_ids.size() / 10) break; + } + mean /= i; + double sd(0); + i = 0; + for (auto & m : map_index2ppm) + { + sd += pow(m.second - mean, 2.0); + ++i; + if (peptide_ids.size() > 1000 && i > peptide_ids.size() / 10) break; + } + sd = sqrt(1.0/(double)i * sd); + cout << "mean ppm error: " << mean << " sd: " << sd << " 3*sd: " << 3*sd << endl; + map_index2ppm.clear(); + + if (generate_decoys) { fdr.apply(peptide_ids); @@ -3997,7 +4346,8 @@ static void scoreShiftedFragments_( } String percolator_executable = getStringOption_("percolator_executable"); - if (!percolator_executable.empty()) + bool sufficient_PSMs_for_score_recalibration = (xl_pi.size() + pep_pi.size()) > 1000; + if (!percolator_executable.empty() && sufficient_PSMs_for_score_recalibration) // only try to call percolator if we have some PSMs { // run percolator on idXML String perc_out = out_idxml; @@ -4079,6 +4429,10 @@ static void scoreShiftedFragments_( } } } + else + { + if (sufficient_PSMs_for_score_recalibration == false) OPENMS_LOG_WARN << "Too few PSMs for score recalibration. Skipped." << endl; + } } else // no decoys { From 8a21e1c3630e624cb6d18bb518f8ca322c6c3579 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 16 Aug 2019 09:40:46 +0200 Subject: [PATCH 074/471] U statistic --- src/utils/OpenNuXL.cpp | 70 ++++++++++++++++++++++++++---------------- 1 file changed, 44 insertions(+), 26 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 4a98cbec5df..d4dcd294e36 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -194,9 +194,6 @@ class AnnotatedHit Mass error is assumed normally distributed with: - mean = 0 - sd = sqrt(precursor_mass_tolerance) => variance = precursor tolerance - Background error (false hits) is assumed uniform in precursor tolerance window. - mass_error_prior_negatives = 1.0 / (2.0 * precursor_mass_tolerance); - mass_error_p = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; */ float mass_error_p = 0; @@ -342,6 +339,7 @@ class AnnotatedHit size_t tag_XLed = 0; // tag that contains the transition from unshifted to shifted double rank_product = 0; + double wTop50 = 0; static bool hasBetterScore(const AnnotatedHit& a, const AnnotatedHit& b) { @@ -667,7 +665,6 @@ class OpenNuXL : const Size N = intensity_sum.size(); std::vector b_ions(N, 0.0), y_ions(N, 0.0); - // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); @@ -1259,7 +1256,7 @@ score += ah.mass_error_p * 1.15386068 static float calculateFastScore(const AnnotatedHit& ah) { - return + 1.0 * ah.total_loss_score + return + 1.0 * ah.total_loss_score /* + 1.0 * ah.total_MIC + 0.333 * ah.mass_error_p*/; } @@ -1420,17 +1417,40 @@ static void scoreShiftedFragments_( } }; + struct RankScores + { + double rp = 0; // normalized intensity rank product + double wTop50 = 0; + }; - double rankProduct_(const MSSpectrum& spectrum, vector peak_matched) + RankScores rankScores_(const MSSpectrum& spectrum, vector peak_matched) { - double rp(0); + double matched = std::accumulate(peak_matched.begin(), peak_matched.end(), 0); + double U1(0); + size_t c1(0); + RankScores r; for (size_t i = 0; i != peak_matched.size(); ++i) { - if (!peak_matched[i]) continue; - const double rank = 1 + spectrum.getIntegerDataArrays()[IA_RANK_INDEX][i]; // ranks start at 0 -> add 1 - rp += 1.0/(double)peak_matched.size() * log((double)rank); + if (!peak_matched[i]) + { + continue; + } + else + { + const double rank = 1 + spectrum.getIntegerDataArrays()[IA_RANK_INDEX][i]; // ranks start at 0 -> add 1 + r.rp += 1.0/matched * log((double)rank); + U1 += rank; + ++c1; + } } - return exp(rp); + U1 -= c1 * (c1 + 1.0) / 2.0; + size_t c2 = peak_matched.size() - c1; + double U2 = c1 * c2 - U1; + double U = std::min(U1, U2); + U = (U - 0.5 * c1 * c2) / sqrt(c1*c2*(c1+c2+1.0)/12.0); // normal approximation of test statistic - not sure if this works for small c1/c2 + r.wTop50 = fabs(U); + r.rp = exp(r.rp - 1.0 / matched * lgamma(matched+1)); // = rp / lowest possible rp given number of matches + return r; } void calculateNucleotideTags_(PeakMap& exp, @@ -2767,6 +2787,7 @@ static void scoreShiftedFragments_( ph.setMetaValue("nucleotide_mass_tags", (double)spec.getFloatDataArrays()[1][0]); ph.setMetaValue("nr_candidates", nr_candidates[scan_index]); ph.setMetaValue("NuXL:rank_product", ah.rank_product); + ph.setMetaValue("NuXL:wTop50", ah.wTop50); ph.setPeakAnnotations(ah.fragment_annotations); ph.setMetaValue("isotope_error", static_cast(ah.isotope_error)); @@ -2924,7 +2945,8 @@ static void scoreShiftedFragments_( << "NuXL:tag_unshifted" << "NuXL:tag_shifted" << "nr_candidates" - << "NuXL:rank_product"; + << "NuXL:rank_product" + << "NuXL:wTop50"; #ifdef OPENNUXL_SEPARATE_FEATURES for (auto & pi : peptide_ids) { @@ -3108,7 +3130,6 @@ static void scoreShiftedFragments_( const vector & total_loss_template_z1_b_ions, const vector & total_loss_template_z1_y_ions, const boost::math::normal & gaussian_mass_error, - const double & mass_error_prior_negatives, const double & fragment_mass_tolerance, const bool & fragment_mass_tolerance_unit_ppm, vector & annotated_hits, @@ -3157,7 +3178,7 @@ static void scoreShiftedFragments_( if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { return; } const double mass_error_ppm = (current_peptide_mass - exp_pc_mass) / exp_pc_mass * 1e6; - const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); // add peptide hit AnnotatedHit ah; @@ -3441,9 +3462,6 @@ static void scoreShiftedFragments_( // with sigma^2 = precursor_mass_tolerance boost::math::normal gaussian_mass_error(0.0, sqrt(precursor_mass_tolerance)); - // random: assumed uniform distribution of mass error - const double mass_error_prior_negatives = 1.0 / (2.0 * precursor_mass_tolerance); - bool precursor_mass_tolerance_unit_ppm = (getStringOption_("precursor:mass_tolerance_unit") == "ppm"); IntList precursor_isotopes = getIntList_("precursor:isotopes"); @@ -3831,8 +3849,7 @@ static void scoreShiftedFragments_( if (badTotalLossScore(hyperScore, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; - const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) - / mass_error_prior_negatives; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); // add peptide hit AnnotatedHit ah; @@ -3859,18 +3876,18 @@ static void scoreShiftedFragments_( ah.sequence_score = ladderScore_(range) / (double)intensity_sum.size(); } - ah.rank_product = rankProduct_(exp_spectrum, peak_matched); + RankScores rankscores = rankScores_(exp_spectrum, peak_matched); + ah.rank_product = rankscores.rp; + ah.wTop50 = rankscores.wTop50; const XLTags longest_tags = getLongestTagWithShift(intensity_sum, vector()); - // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one - if (longest_tags.tag_XLed == 0) continue; + if (longest_tags.tag_unshifted == 0) continue; ah.tag_XLed = longest_tags.tag_XLed; ah.tag_unshifted = longest_tags.tag_unshifted; ah.tag_shifted = longest_tags.tag_shifted; - // combined score const double tags = exp_spectrum.getFloatDataArrays()[1][0]; ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); @@ -4030,7 +4047,7 @@ static void scoreShiftedFragments_( } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; - const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / mass_error_prior_negatives; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); // add peptide hit AnnotatedHit ah; @@ -4070,7 +4087,9 @@ static void scoreShiftedFragments_( const XLTags longest_tags = getLongestTagWithShift(intensity_linear, intensity_xls); - ah.rank_product = rankProduct_(exp_spectrum, peak_matched); + RankScores rankscores = rankScores_(exp_spectrum, peak_matched); + ah.rank_product = rankscores.rp; + ah.wTop50 = rankscores.wTop50; ah.tag_XLed = longest_tags.tag_XLed; ah.tag_unshifted = longest_tags.tag_unshifted; @@ -4136,7 +4155,6 @@ static void scoreShiftedFragments_( total_loss_template_z1_b_ions, total_loss_template_z1_y_ions, gaussian_mass_error, - mass_error_prior_negatives, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, annotated_peptides[scan_index], From 6c5728b612f1d041d53c3ab9cbcadeb1d8521f90 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 13 Sep 2019 10:43:52 +0200 Subject: [PATCH 075/471] strict mass filtering --- src/utils/OpenNuXL.cpp | 392 ++++++++++++++++++++++++++++------------- 1 file changed, 271 insertions(+), 121 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index d4dcd294e36..f5f3789847c 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -381,6 +381,7 @@ class OpenNuXL : static constexpr double MIN_SHIFTED_IONS = 1; // minimum number of matches to shifted ions (applies to XLs only) static constexpr Size IA_CHARGE_INDEX = 0; static constexpr Size IA_RANK_INDEX = 1; + static constexpr Size IA_DENOVO_TAG_INDEX = 2; protected: void registerOptionsAndFlags_() override @@ -540,7 +541,7 @@ class OpenNuXL : static bool badPartialLossScore(float tlss_Morph, float plss_Morph, float plss_MIC, float plss_im_MIC, float plss_pc_MIC, float marker_ions_score) { - if (plss_Morph + tlss_Morph < 5.03) return true; + if (plss_Morph + tlss_Morph < 5.03) return true; // less than 5 peaks? 3% TIC if (plss_MIC + plss_im_MIC + plss_pc_MIC + marker_ions_score < 0.03) return true; @@ -643,6 +644,8 @@ class OpenNuXL : const double fragment_mass_tolerance, const bool fragment_mass_tolerance_unit_ppm, std::vector& intensity_sum, + std::vector& b_ions, + std::vector& y_ions, vector& peak_matched, float& hyperScore, float& MIC, @@ -657,13 +660,13 @@ class OpenNuXL : OPENMS_PRECONDITION(total_loss_template_z1_b_ions.size() == total_loss_template_z1_y_ions.size(), "b- and y-ion arrays must have same size."); OPENMS_PRECONDITION(total_loss_template_z1_b_ions.size() > 0, "b- and y-ion arrays must not be empty."); OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); - OPENMS_PRECONDITION(intensity_sum.size() == total_loss_template_z1_y_ions.size(), "Sum array needs to be of same size as y-ion array"); + OPENMS_PRECONDITION(intensity_sum.size() == b_ions.size(), "Sum array needs to be of same size as b-ion array"); + OPENMS_PRECONDITION(intensity_sum.size() == y_ions.size(), "Sum array needs to be of same size as y-ion array"); OPENMS_PRECONDITION(peak_matched.size() == exp_spectrum.size(), "Peak matched needs to be of same size as experimental spectrum"); OPENMS_PRECONDITION(std::count_if(peak_matched.begin(), peak_matched.end(), [](bool b){return b == true;}) == 0;, "Peak matched must be initialized to false"); double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); - std::vector b_ions(N, 0.0), y_ions(N, 0.0); // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); @@ -911,6 +914,8 @@ class OpenNuXL : const PeakSpectrum& exp_spectrum, const DataArrays::IntegerDataArray& exp_charges, std::vector& intensity_sum, + std::vector& b_ions, + std::vector& y_ions, std::vector& peak_matched, float& plss_hyperScore, float& plss_MIC, @@ -924,12 +929,13 @@ class OpenNuXL : OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_y_ions.size(), "Sum array needs to be of same size as y-ion array"); + OPENMS_PRECONDITION(intensity_sum.size() == b_ions.size(), "Sum array needs to be of same size as b-ion array"); + OPENMS_PRECONDITION(intensity_sum.size() == y_ions.size(), "Sum array needs to be of same size as y-ion array"); OPENMS_PRECONDITION(partial_loss_template_z1_b_ions.size() == partial_loss_template_z1_y_ions.size(), "b- and y-ion arrays must have same size."); OPENMS_PRECONDITION(partial_loss_template_z1_b_ions.size() > 0, "b- and y-ion arrays must not be empty."); double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 - std::vector b_ions(N, 0.0), y_ions(N, 0.0); // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); @@ -1229,6 +1235,8 @@ score += ah.mass_error_p * 1.15386068 //TODO: check Alex if (ah.Morph + ah.pl_Morph < 5.03) return 0; // return ah.total_MIC + ah.marker_ions_score + fraction_of_top50annotated; + +/* return 10.0 * ah.total_loss_score + ah.partial_loss_score + 0.01 * ah.mass_error_p @@ -1237,6 +1245,15 @@ score += ah.mass_error_p * 1.15386068 + 3.0 * ah.pl_MIC + isXL * 3.0 * ah.marker_ions_score + 3.0 * ah.total_MIC + ah.ladder_score; +*/ + return + 10.0 * ah.total_loss_score + + 0.1 * ah.mass_error_p + - 10.0 * ah.err + - 10.0 * ah.pl_err + + 3.0 * ah.pl_MIC + + isXL * 3.0 * ah.marker_ions_score + + 3.0 * ah.total_MIC + ah.ladder_score; /* -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err @@ -1263,26 +1280,28 @@ score += ah.mass_error_p * 1.15386068 /* * Score fragments carrying NA adducts */ -static void scoreShiftedFragments_( - const vector &partial_loss_modification, - const ImmoniumIonsInPeptide& iip, - const PeakSpectrum &exp_spectrum, - const double peptide_mass_without_NA, - double fragment_mass_tolerance, - bool fragment_mass_tolerance_unit_ppm, - const vector &partial_loss_template_z1_b_ions, - const vector &partial_loss_template_z1_y_ions, - const PeakSpectrum &marker_ions_sub_score_spectrum_z1, - vector& intensity_sum, - vector& matched_peaks, - float &partial_loss_sub_score, - float &marker_ions_sub_score, - float &plss_MIC, - float &plss_err, - float &plss_Morph, - float &plss_modds, - float &plss_pc_MIC, - float &plss_im_MIC) +static void scoreXLIons_( + const vector &partial_loss_modification, + const ImmoniumIonsInPeptide& iip, + const PeakSpectrum &exp_spectrum, + const double peptide_mass_without_NA, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const vector &partial_loss_template_z1_b_ions, + const vector &partial_loss_template_z1_y_ions, + const PeakSpectrum &marker_ions_sub_score_spectrum_z1, + vector& intensity_sum, + vector& b_ions, + vector& y_ions, + vector& matched_peaks, + float &partial_loss_sub_score, + float &marker_ions_sub_score, + float &plss_MIC, + float &plss_err, + float &plss_Morph, + float &plss_modds, + float &plss_pc_MIC, + float &plss_im_MIC) { OPENMS_PRECONDITION(!partial_loss_template_z1_b_ions.empty(), "Empty partial loss spectrum provided."); OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); @@ -1314,6 +1333,8 @@ static void scoreShiftedFragments_( exp_spectrum, exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], intensity_sum, + b_ions, + y_ions, matched_peaks, partial_loss_sub_score, plss_MIC, @@ -1330,67 +1351,106 @@ static void scoreShiftedFragments_( if (plss_err > ft_da) plss_err = ft_da; } + // De novo tagger class OPENMS_DLLAPI OpenNuXLTagger { public: - // initalize tagger with minimum/maximum tag length and +- tolerance ppm - OpenNuXLTagger(float ppm, size_t min_tag_length = 3, size_t max_tag_length = 65535) + + // initalize tagger with minimum/maximum tag length and +- tolerance ppm + OpenNuXLTagger(float tol = 0.05, size_t min_tag_length = 0, size_t max_tag_length = 65535) { - ppm_ = ppm; + tol_ = tol; min_tag_length_ = min_tag_length; max_tag_length_ = max_tag_length; - const std::set aas = ResidueDB::getInstance()->getResidues(); + const std::set aas = ResidueDB::getInstance()->getResidues("Natural19WithoutI"); for (const auto& r : aas) { const char letter = r->getOneLetterCode()[0]; const float mass = r->getMonoWeight(Residue::Internal); mass2aa[mass] = letter; - //cout << "Mass: " << mass << "\t" << letter << endl; +#ifdef DEBUG_OPENNUXL_TAGGER + cout << "Mass: " << mass << "\t" << letter << endl; +#endif } - min_gap_ = mass2aa.begin()->first - Math::ppmToMass(ppm, mass2aa.begin()->first); - max_gap_ = mass2aa.rbegin()->first + Math::ppmToMass(ppm, mass2aa.rbegin()->first); + + min_gap_ = mass2aa.begin()->first - tol; + max_gap_ = mass2aa.rbegin()->first + tol; + +#ifdef DEBUG_OPENNUXL_TAGGER + TheoreticalSpectrumGenerator test; + auto param = test.getParameters(); + param.setValue("add_first_prefix_ion", "true"); + param.setValue("add_abundant_immonium_ions", "false"); // we add them manually for charge 1 + param.setValue("add_precursor_peaks", "true"); + param.setValue("add_all_precursor_charges", "false"); // we add them manually for every charge + param.setValue("add_metainfo", "false"); + param.setValue("add_a_ions", "false"); + param.setValue("add_b_ions", "true"); + param.setValue("add_c_ions", "false"); + param.setValue("add_x_ions", "false"); + param.setValue("add_y_ions", "true"); + param.setValue("add_z_ions", "false"); + test.setParameters(param); + MSSpectrum test_s; + test.getSpectrum(test_s, AASequence::fromString("TESTPEPTIDE"), 1, 1); + cout << "should be ESTPEPTIDE:" << getLongestTag(test_s) << endl; +#endif } - void getTag(const std::vector& mzs, std::set& tags) const - { - // start peak - std::string tag; - if (min_tag_length_ > mzs.size()) return; // avoid segfault + void getTag(const std::vector& mzs, std::set& tags) const + { + // start peak + if (min_tag_length_ > mzs.size()) return; // avoid segfault - for (size_t i = 0; i < mzs.size() - min_tag_length_; ++i) + std::string tag; + for (size_t i = 0; i < mzs.size() - min_tag_length_; ++i) + { + getTag_(tag, mzs, i, tags); + tag.clear(); + } + } + + // generate tags from mass vector @mzs using the standard residues in ResidueDB + void getTag(const MSSpectrum& spec, std::set& tags) const { - getTag_(tag, mzs, i, tags); - tag.clear(); + const size_t N = spec.size(); + if (N < min_tag_length_) { return; } + // copy to float vector (speed) + std::vector mzs; + mzs.reserve(N); + for (auto const& p : spec) { mzs.push_back(p.getMZ()); } + getTag(mzs, tags); } - } - // generate tags from mass vector @mzs using the standard residues in ResidueDB - void getTag(const MSSpectrum& spec, std::set& tags) const - { - const size_t N = spec.size(); - if (N < min_tag_length_) { return; } - // copy to float vector (speed) - std::vector mzs; - mzs.reserve(N); - for (auto const& p : spec) { mzs.push_back(p.getMZ()); } - getTag(mzs, tags); - } + // generate tags from mass vector @mzs using the standard residues in ResidueDB + std::string getLongestTag(const MSSpectrum& spec) const + { + std::set tags; + getTag(spec, tags); + if (tags.empty()) return ""; + //cout << "Ntags:" << tags.size() << endl; + //for (const auto & s: tags) { cout << s << endl; } + const auto longest = std::max_element(tags.cbegin(), tags.cend(), + [](const std::string& lhs, const std::string& rhs) { return lhs.size() < rhs.size(); }); + //cout << "longest:" << *longest << endl; + return *longest; + } private: float min_gap_; // will be set to smallest residue mass in ResidueDB float max_gap_; // will be set to highest residue mass in ResidueDB - float ppm_; // < tolerance + float tol_; // < tolerance size_t min_tag_length_; // < minimum tag length size_t max_tag_length_; // < maximum tag length std::map mass2aa; + char getAAByMass_(float m) const { // fast check for border cases if (m < min_gap_ || m > max_gap_) return ' '; - const float delta = Math::ppmToMass(ppm_, m); - auto left = mass2aa.lower_bound(m - delta); + auto left = mass2aa.lower_bound(m - tol_); //if (left == mass2aa.end()) return ' '; // cannot happen, since we checked boundaries above - if (fabs(left->second - m) < delta) return left->second; + if (fabs(left->first - m) < tol_) return left->second; return ' '; } @@ -1404,9 +1464,12 @@ static void scoreShiftedFragments_( if (tag.size() == max_tag_length_) { return; } // maximum tag size reached? - continue with next parent const float gap = mzs[j] - mzs[i]; - //cout << i << "\t" << j << "\t" << mzs[i] << "\t" << mzs[j] << "\t" << gap << endl; if (gap > max_gap_) { return; } // already too far away - continue with next parent const char aa = getAAByMass_(gap); +#ifdef DEBUG_OPENNUXL_TAGGER + cout << i << "\t" << j << "\t" << mzs[i] << "\t" << mzs[j] << "\t" << gap << "\t'" << aa << "'" << endl; +#endif + if (aa == ' ') { ++j; continue; } // can't extend tag tag += aa; getTag_(tag, mzs, j, tags); @@ -1423,11 +1486,38 @@ static void scoreShiftedFragments_( double wTop50 = 0; }; + + class SmallestElements + { + private: + int max_size_; + public: + priority_queue, std::greater> pq; + SmallestElements(size_t size): + max_size_(size) + { + pq = priority_queue, std::greater>(); // smallest element at top + } + + void tryAdd(size_t v) + { + if (pq.size() < max_size_) + { + pq.push(v); + return; + } + if (v < pq.top()) + { + pq.pop(); //get rid of the root + pq.push(v); //priority queue will automatically restructure + } + } +}; + RankScores rankScores_(const MSSpectrum& spectrum, vector peak_matched) { double matched = std::accumulate(peak_matched.begin(), peak_matched.end(), 0); - double U1(0); - size_t c1(0); + SmallestElements top7ranks(7); RankScores r; for (size_t i = 0; i != peak_matched.size(); ++i) { @@ -1439,16 +1529,18 @@ static void scoreShiftedFragments_( { const double rank = 1 + spectrum.getIntegerDataArrays()[IA_RANK_INDEX][i]; // ranks start at 0 -> add 1 r.rp += 1.0/matched * log((double)rank); - U1 += rank; - ++c1; + top7ranks.tryAdd(rank); } } - U1 -= c1 * (c1 + 1.0) / 2.0; - size_t c2 = peak_matched.size() - c1; - double U2 = c1 * c2 - U1; - double U = std::min(U1, U2); - U = (U - 0.5 * c1 * c2) / sqrt(c1*c2*(c1+c2+1.0)/12.0); // normal approximation of test statistic - not sure if this works for small c1/c2 - r.wTop50 = fabs(U); + + size_t median = peak_matched.size() / 2; // init to number of peaks / 2 + for (size_t i = 1; i <= 4; ++i) + { + if (top7ranks.pq.empty()) break; + median = top7ranks.pq.top(); + top7ranks.pq.pop(); + } + r.wTop50 = median; r.rp = exp(r.rp - 1.0 / matched * lgamma(matched+1)); // = rp / lowest possible rp given number of matches return r; } @@ -1551,8 +1643,9 @@ static void scoreShiftedFragments_( spec.getFloatDataArrays()[1].push_back((double)match / (double)in_mass_range); spec.getFloatDataArrays()[1].setName("nucleotide_mass_tags"); - spec.getIntegerDataArrays().resize(2); - // calculate ranks + spec.getIntegerDataArrays().resize(3); + + // calculate ranks // // initialize original index locations vector idx(spec.size()); @@ -1564,6 +1657,12 @@ static void scoreShiftedFragments_( for (int rank : idx) spec.getIntegerDataArrays()[IA_RANK_INDEX].push_back(rank); spec.getIntegerDataArrays()[IA_RANK_INDEX].setName("intensity_rank"); + + OpenNuXLTagger tagger(0.05, 3); + spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].push_back(tagger.getLongestTag(spec).size()); + spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].setName("longest_tag"); + //cout << "tag length:" << spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] << endl; + } /* for (const auto& mra : aa_plus_adduct_mass) @@ -2785,6 +2884,9 @@ static void scoreShiftedFragments_( } ph.setMetaValue("nucleotide_mass_tags", (double)spec.getFloatDataArrays()[1][0]); + // proportion of longest amino acid tag to identified sequence size +// ph.setMetaValue("NuXL:aminoacid_max_tag", (double)spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] / (double)s.size()); + ph.setMetaValue("NuXL:aminoacid_max_tag", (double)spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] / ((double)s.size()*ah.ladder_score)); ph.setMetaValue("nr_candidates", nr_candidates[scan_index]); ph.setMetaValue("NuXL:rank_product", ah.rank_product); ph.setMetaValue("NuXL:wTop50", ah.wTop50); @@ -2944,6 +3046,7 @@ static void scoreShiftedFragments_( << "NuXL:tag_XLed" << "NuXL:tag_unshifted" << "NuXL:tag_shifted" + << "NuXL:aminoacid_max_tag" << "nr_candidates" << "NuXL:rank_product" << "NuXL:wTop50"; @@ -3116,7 +3219,7 @@ static void scoreShiftedFragments_( } } - // calculate PSMs using total loss scoring (no NA-shifted fragments) + // calculate PSMs using total loss scoring (no NA-shifted fragments) - used in fast scoring static void addPSMsTotalLossScoring_( const PeakSpectrum& exp_spectrum, const StringView sequence, @@ -3149,6 +3252,8 @@ static void scoreShiftedFragments_( im_MIC(0); vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); + vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); vector peak_matched(exp_spectrum.size(), false); scorePeptideIons_( @@ -3162,6 +3267,8 @@ static void scoreShiftedFragments_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, intensity_sum, + b_ions, + y_ions, peak_matched, total_loss_score, tlss_MIC, @@ -3387,7 +3494,6 @@ static void scoreShiftedFragments_( XLTags getLongestTagWithShift(const vector& intL, const vector& intXL) { // calculate longest consecutive unshifted / shifted sequence and longest sequence spanning unshifted + shifted residues - // Note to myself: kind of nice and simple algorithm by the way ;) XLTags tags; vector runL(intL.size(), 0); size_t run(0); @@ -3398,8 +3504,9 @@ static void scoreShiftedFragments_( runL[l] = run; if (run > tags.tag_unshifted) tags.tag_unshifted = run; } - + // tags.tag_unshifted contains longest run // runL[i] now contains current run length e.g.: 000123400100 + if (!intXL.empty()) { vector runX(intXL.size(), 0); @@ -3411,9 +3518,9 @@ static void scoreShiftedFragments_( runX[x] = run; if (run > tags.tag_shifted) tags.tag_shifted = run; } + // tags.tag_shifted contains longest run // runX[i] now contains the longest run in X starting at position i e.g.: 00003210000 - //vector runLX(intX.size(), 0); size_t maximum_tag_length(0); // calculate maximum tag that spans linear intensities and at least one XLed amino acid for (Size i = 0; i < intXL.size() - 1; ++i) @@ -3788,6 +3895,10 @@ static void scoreShiftedFragments_( generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::ResidueType::YIon, total_loss_template_z1_y_ions); } + + //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + // all ion scoring + // if (!fast_scoring_) { // retrieve NA adduct name @@ -3822,7 +3933,10 @@ static void scoreShiftedFragments_( pc_MIC(0), im_MIC(0); - vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); + vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); + vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); + vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); + vector peak_matched(exp_spectrum.size(), false); scorePeptideIons_( exp_spectrum, @@ -3834,7 +3948,9 @@ static void scoreShiftedFragments_( iip, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - intensity_sum, + intensity_linear, + b_ions, + y_ions, peak_matched, hyperScore, tlss_MIC, @@ -3868,19 +3984,19 @@ static void scoreShiftedFragments_( ah.rna_mod_index = rna_mod_index; ah.isotope_error = isotope_error; - auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); - ah.ladder_score = ladderScore_(range) / (double)intensity_sum.size(); - range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); + auto range = make_pair(intensity_linear.begin(), intensity_linear.end()); + ah.ladder_score = ladderScore_(range) / (double)intensity_linear.size(); + range = longestCompleteLadder_(intensity_linear.begin(), intensity_linear.end()); if (range.second != range.first) { - ah.sequence_score = ladderScore_(range) / (double)intensity_sum.size(); + ah.sequence_score = ladderScore_(range) / (double)intensity_linear.size(); } RankScores rankscores = rankScores_(exp_spectrum, peak_matched); ah.rank_product = rankscores.rp; ah.wTop50 = rankscores.wTop50; - const XLTags longest_tags = getLongestTagWithShift(intensity_sum, vector()); + const XLTags longest_tags = getLongestTagWithShift(intensity_linear, vector()); if (longest_tags.tag_unshifted == 0) continue; @@ -3960,13 +4076,13 @@ static void scoreShiftedFragments_( for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; - // count candidate for spectrum #ifdef _OPENMP - omp_set_lock(&(annotated_peptides_lock[scan_index])); - omp_set_lock(&(annotated_XLs_lock[scan_index])); - ++nr_candidates[scan_index]; - omp_unset_lock(&(annotated_XLs_lock[scan_index])); - omp_unset_lock(&(annotated_peptides_lock[scan_index])); + omp_set_lock(&(annotated_peptides_lock[scan_index])); + omp_set_lock(&(annotated_XLs_lock[scan_index])); + // count candidate for spectrum + ++nr_candidates[scan_index]; + omp_unset_lock(&(annotated_XLs_lock[scan_index])); + omp_unset_lock(&(annotated_peptides_lock[scan_index])); #endif const int & isotope_error = l->second.second; const PeakSpectrum & exp_spectrum = spectra[scan_index]; @@ -3982,8 +4098,10 @@ static void scoreShiftedFragments_( const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); - vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); + vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); vector peak_matched(exp_spectrum.size(), false); + vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); // b & a ions + vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); scorePeptideIons_( exp_spectrum, @@ -3996,6 +4114,8 @@ static void scoreShiftedFragments_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, intensity_linear, + b_ions, + y_ions, peak_matched, hyperScore, tlss_MIC, @@ -4018,25 +4138,30 @@ static void scoreShiftedFragments_( plss_pc_MIC(0), plss_im_MIC(0); - scoreShiftedFragments_( partial_loss_modification, - iip, - exp_spectrum, - current_peptide_mass_without_NA, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - partial_loss_template_z1_bions, - partial_loss_template_z1_yions, - marker_ions_sub_score_spectrum_z1, - intensity_xls, - peak_matched, - partial_loss_sub_score, - marker_ions_sub_score, - plss_MIC, - plss_err, - plss_Morph, - plss_modds, - plss_pc_MIC, - plss_im_MIC); + std::fill(b_ions.begin(), b_ions.end(), 0); + std::fill(y_ions.begin(), y_ions.end(), 0); + + scoreXLIons_(partial_loss_modification, + iip, + exp_spectrum, + current_peptide_mass_without_NA, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + partial_loss_template_z1_bions, + partial_loss_template_z1_yions, + marker_ions_sub_score_spectrum_z1, + intensity_xls, + b_ions, + y_ions, + peak_matched, + partial_loss_sub_score, + marker_ions_sub_score, + plss_MIC, + plss_err, + plss_Morph, + plss_modds, + plss_pc_MIC, + plss_im_MIC); const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC + marker_ions_sub_score; @@ -4055,6 +4180,17 @@ static void scoreShiftedFragments_( ah.sequence = *cit; // copy StringView ah.peptide_mod_index = mod_pep_idx; + +/* +/////////////////////////////////////////////////////////////////////////////// test recalculate hyperscore on merged XL/non-XL ladders + size_t y_ion_count = std::count_if(y_ions.begin(), y_ions.end(), [](double d) { return d > 1e-6; }); + size_t b_ion_count = std::count_if(b_ions.begin(), b_ions.end(), [](double d) { return d > 1e-6; }); + size_t dot_product = std::accumulate(intensity_xls.begin(), intensity_xls.end(), 0.0); + dot_product = std::accumulate(intensity_linear.begin(), intensity_linear.end(), dot_product); + const double yFact = logfactorial_(y_ion_count); + const double bFact = logfactorial_(b_ion_count); + hyperScore = log1p(dot_product) + yFact + bFact; +*/ ah.total_loss_score = hyperScore; ah.MIC = tlss_MIC; ah.immonium_score = im_MIC; @@ -4096,7 +4232,7 @@ static void scoreShiftedFragments_( ah.tag_shifted = longest_tags.tag_shifted; // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one - if (longest_tags.tag_XLed == 0) continue; + if (longest_tags.tag_XLed == 0) { continue; } // combined score const double tags = exp_spectrum.getFloatDataArrays()[1][0]; @@ -4267,39 +4403,53 @@ static void scoreShiftedFragments_( // annotate RNPxl related information to hits and create report vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); - // determine average mass error / sd (needs to be after annotate for now) +/* + // keep 10 bins with best 100 scores using priority queues + vector best_score_per_bin(10, LargestElements(100)); + for (size_t index = 0; index != peptide_ids.size(); ++index) + { + size_t bin_index = 10.0 * index / (double)peptide_ids.size(); + if (peptide_ids[index].getHits().empty()) continue; + if (peptide_ids[index].getHits()[0].getMetaValue("target_decoy") == "target") + { + best_score_per_bin[bin_index].tryAdd(peptide_ids[index].getHits()[0].getScore()); + } + } +*/ map> map_index2ppm; + size_t i(0); + double mean(0); for (size_t index = 0; index != peptide_ids.size(); ++index) { if (peptide_ids[index].getHits().empty()) continue; - if (peptide_ids[index].getHits()[0].getMetaValue("target_decoy") == "target") + if (peptide_ids[index].getHits()[0].getMetaValue("target_decoy") == "target" + && (double)peptide_ids[index].getHits()[0].getMetaValue("NuXL:total_loss_score") > 15.0) // not too bad score { double ppm_error = peptide_ids[index].getHits()[0].getMetaValue(OpenMS::Constants::PRECURSOR_ERROR_PPM_USERPARAM); map_index2ppm[peptide_ids[index].getHits()[0].getScore()] = ppm_error; + mean += ppm_error; + ++i; } } - - size_t i(0); - double mean(0); - for (auto & m : map_index2ppm) - { - mean += m.second; - ++i; - if (peptide_ids.size() > 1000 && i > peptide_ids.size() / 10) break; - } mean /= i; double sd(0); - i = 0; for (auto & m : map_index2ppm) { sd += pow(m.second - mean, 2.0); - ++i; - if (peptide_ids.size() > 1000 && i > peptide_ids.size() / 10) break; } sd = sqrt(1.0/(double)i * sd); cout << "mean ppm error: " << mean << " sd: " << sd << " 3*sd: " << 3*sd << endl; - map_index2ppm.clear(); + // as we are dealing with a very large search space, filter out all identifications with mass error > 3 *sd + peptide_ids.erase( + std::remove_if(peptide_ids.begin(), peptide_ids.end(), + [&sd, &mean](const PeptideIdentification & pi) + { + return fabs((double)pi.getHits()[0].getMetaValue(OpenMS::Constants::PRECURSOR_ERROR_PPM_USERPARAM)) - fabs(mean) > 3*sd; + }), + peptide_ids.end()); + + map_index2ppm.clear(); if (generate_decoys) { From c6b018d165a70b6ea3fe93099336e69c7815b554 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 16 Sep 2019 14:56:54 +0200 Subject: [PATCH 076/471] broken!!!!!!!!!! --- src/utils/OpenNuXL.cpp | 84 +++++++++++++++++++++++++++++++----------- 1 file changed, 63 insertions(+), 21 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index f5f3789847c..6c24c7eaa0a 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -3495,38 +3495,70 @@ static void scoreXLIons_( { // calculate longest consecutive unshifted / shifted sequence and longest sequence spanning unshifted + shifted residues XLTags tags; - vector runL(intL.size(), 0); + vector prefixRunL(intL.size(), 0); size_t run(0); for (int l = 0; l != intL.size(); ++l) { if (intL[l] == 0) { run = 0; continue; } ++run; - runL[l] = run; + prefixRunL[l] = run; if (run > tags.tag_unshifted) tags.tag_unshifted = run; } // tags.tag_unshifted contains longest run - // runL[i] now contains current run length e.g.: 000123400100 + // prefixRunL[i] now contains current run length e.g.: 000123400100 for prefix ions + + vector suffixRunL(intL.size(), 0); + run = 0; + for (int l = (int)intL.size() - 1; l >= 0; --l) + { + if (intL[l] == 0) { run = 0; continue; } + ++run; + suffixRunL[l] = run; + } + // suffixRunL[i] now contains current run length e.g.: 000432100100 for suffix ions if (!intXL.empty()) { - vector runX(intXL.size(), 0); + // for XL we calculate the runs in reverse order so we can later quickly calculate the maximum run + // through non-cross-linked and cross-linked ions + + vector prefixRunX(intXL.size(), 0); run = 0; for (int x = (int)intXL.size() - 1; x >= 0; --x) // note the reverse order { if (intXL[x] == 0) { run = 0; continue; } ++run; - runX[x] = run; + prefixRunX[x] = run; if (run > tags.tag_shifted) tags.tag_shifted = run; } // tags.tag_shifted contains longest run - // runX[i] now contains the longest run in X starting at position i e.g.: 00003210000 + // prefixRunX[i] now contains the longest run in X starting at position i e.g.: 00003210000 for prefix ions + vector suffixRunX(intXL.size(), 0); + run = 0; + for (int x = 0; x != (int)intXL.size(); ++x) + { + if (intXL[x] == 0) { run = 0; continue; } + ++run; + suffixRunX[x] = run; + } + // suffixRunX[i] now contains the longest run in X starting at position i e.g.: 00001230000 for suffix ions + size_t maximum_tag_length(0); - // calculate maximum tag that spans linear intensities and at least one XLed amino acid + + // calculate maximum tag that spans linear intensities and at least one XLed amino acid for prefix ions for (Size i = 0; i < intXL.size() - 1; ++i) { - if (runX[i + 1] == 0 || runL[i] == 0) continue; // must have one cross-linked amino acid next to non-cross-linked amino acid - const size_t tag_length = runL[i] + runX[i + 1]; // tag length if cross-link is introduced at amino acid i+1 + if (prefixRunX[i + 1] == 0 || prefixRunL[i] == 0) continue; // must have one cross-linked amino acid next to non-cross-linked amino acid + const size_t tag_length = prefixRunL[i] + prefixRunX[i + 1]; // tag length if cross-link is introduced at amino acid i+1 + if (tag_length > maximum_tag_length) maximum_tag_length = tag_length; + } + + // same for suffix ions + for (Size i = 1; i <= intXL.size() - 1; ++i) + { + if (suffixRunX[i] == 0 || suffixRunL[i + 1] == 0) continue; // must have one cross-linked amino acid next to non-cross-linked amino acid + const size_t tag_length = suffixRunX[i] + suffixRunL[i + 1]; // tag length with cross-linked part and non-cross-linked if (tag_length > maximum_tag_length) maximum_tag_length = tag_length; } tags.tag_XLed = maximum_tag_length; @@ -3534,7 +3566,6 @@ static void scoreXLIons_( return tags; } - ExitCodes main_(int, const char**) override { ProgressLogger progresslogger; @@ -3886,7 +3917,6 @@ static void scoreXLIons_( if (low_it == up_it) { continue; } // no matching precursor in data - // add peaks for b- and y- ions with charge 1 (sorted by m/z) // total / complete loss spectra are generated for fast and (slow) full scoring if (total_loss_template_z1_b_ions.empty()) // only create complete loss spectrum once as this is rather costly and need only to be done once per petide @@ -3912,6 +3942,11 @@ static void scoreXLIons_( for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; + const PeakSpectrum & exp_spectrum = spectra[scan_index]; + + // require at least one mass tag + if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } + // count candidate for spectrum #ifdef _OPENMP omp_set_lock(&(annotated_peptides_lock[scan_index])); @@ -3922,7 +3957,6 @@ static void scoreXLIons_( #endif //const double exp_pc_mass = l->first; const int & isotope_error = l->second.second; - const PeakSpectrum & exp_spectrum = spectra[scan_index]; const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); float hyperScore(0), @@ -4076,6 +4110,9 @@ static void scoreXLIons_( for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; + const PeakSpectrum & exp_spectrum = spectra[scan_index]; + // require at least one mass tag + if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } #ifdef _OPENMP omp_set_lock(&(annotated_peptides_lock[scan_index])); omp_set_lock(&(annotated_XLs_lock[scan_index])); @@ -4085,7 +4122,6 @@ static void scoreXLIons_( omp_unset_lock(&(annotated_peptides_lock[scan_index])); #endif const int & isotope_error = l->second.second; - const PeakSpectrum & exp_spectrum = spectra[scan_index]; float tlss_MIC(0), tlss_err(1.0), tlss_Morph(0), @@ -4440,14 +4476,20 @@ static void scoreXLIons_( sd = sqrt(1.0/(double)i * sd); cout << "mean ppm error: " << mean << " sd: " << sd << " 3*sd: " << 3*sd << endl; - // as we are dealing with a very large search space, filter out all identifications with mass error > 3 *sd - peptide_ids.erase( - std::remove_if(peptide_ids.begin(), peptide_ids.end(), - [&sd, &mean](const PeptideIdentification & pi) - { - return fabs((double)pi.getHits()[0].getMetaValue(OpenMS::Constants::PRECURSOR_ERROR_PPM_USERPARAM)) - fabs(mean) > 3*sd; - }), - peptide_ids.end()); + // as we are dealing with a very large search space, filter out all identifications with mass error > 5 *sd + + for (size_t index = 0; index != peptide_ids.size(); ++index) + { + vector& phs = peptide_ids[index].getHits(); + if (phs.empty()) continue; + phs.erase( + std::remove_if(phs.begin(), phs.end(), + [&sd, &mean](const PeptideHit & ph) + { + return fabs((double)ph.getMetaValue(OpenMS::Constants::PRECURSOR_ERROR_PPM_USERPARAM)) - fabs(mean) > 5*sd; + }), + phs.end()); + } map_index2ppm.clear(); From 67393ae3a7b09ceb8e2e688229071e94ef2ed10a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 27 Sep 2019 13:13:54 +0200 Subject: [PATCH 077/471] raw perc fast 232-3 329/9 slow 195-0 288/2 --- src/utils/OpenNuXL.cpp | 47 +++++++++++++++++++++++++++++------------- 1 file changed, 33 insertions(+), 14 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 9af3a0dc632..a9618468210 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -546,7 +546,7 @@ class OpenNuXL : if (plss_MIC + plss_im_MIC + plss_pc_MIC + marker_ions_score < 0.03) return true; // if we don't see shifted ladder ions, we need at least some signal in the shifted immonium ions - return (plss_Morph < MIN_SHIFTED_IONS + 1.0 && plss_im_MIC < 0.03); + return (plss_Morph < MIN_SHIFTED_IONS && plss_im_MIC < 0.03); } /* @@ -1640,7 +1640,9 @@ static void scoreXLIons_( } spec.getFloatDataArrays().resize(2); - spec.getFloatDataArrays()[1].push_back((double)match / (double)in_mass_range); + + spec.getFloatDataArrays()[1].resize(1); + spec.getFloatDataArrays()[1][0] = (double)match / (double)in_mass_range; spec.getFloatDataArrays()[1].setName("nucleotide_mass_tags"); spec.getIntegerDataArrays().resize(3); @@ -1654,15 +1656,15 @@ static void scoreXLIons_( // sort indexes based on comparing intensity values (0 = highest intensity) sort(idx.begin(), idx.end(), [&spec](size_t i1, size_t i2) { return spec[i1].getIntensity() > spec[i2].getIntensity(); }); - - for (int rank : idx) spec.getIntegerDataArrays()[IA_RANK_INDEX].push_back(rank); + + spec.getIntegerDataArrays()[IA_RANK_INDEX].clear(); + for (int rank : idx) { spec.getIntegerDataArrays()[IA_RANK_INDEX].push_back(rank); } spec.getIntegerDataArrays()[IA_RANK_INDEX].setName("intensity_rank"); OpenNuXLTagger tagger(0.05, 3); - spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].push_back(tagger.getLongestTag(spec).size()); + spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].resize(1); + spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = tagger.getLongestTag(spec).size(); spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].setName("longest_tag"); - //cout << "tag length:" << spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] << endl; - } /* for (const auto& mra : aa_plus_adduct_mass) @@ -2885,10 +2887,10 @@ static void scoreXLIons_( } ph.setMetaValue("nucleotide_mass_tags", (double)spec.getFloatDataArrays()[1][0]); - // proportion of longest amino acid tag to identified sequence size -// ph.setMetaValue("NuXL:aminoacid_max_tag", (double)spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] / (double)s.size()); - ph.setMetaValue("NuXL:aminoacid_max_tag", spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0]); - ph.setMetaValue("NuXL:aminoacid_id_to_max_tag_ratio", (ah.ladder_score * s.size()) / (double)spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0]); + int maxtag = spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0]; + ph.setMetaValue("NuXL:aminoacid_max_tag", maxtag); + const double id2maxtag = maxtag == 0 ? 0 : (ah.ladder_score * s.size()) / (double)maxtag; + ph.setMetaValue("NuXL:aminoacid_id_to_max_tag_ratio", id2maxtag); ph.setMetaValue("nr_candidates", nr_candidates[scan_index]); ph.setMetaValue("NuXL:rank_product", ah.rank_product); ph.setMetaValue("NuXL:wTop50", ah.wTop50); @@ -3589,7 +3591,7 @@ static void scoreXLIons_( String in_db = getStringOption_("database"); String out_idxml = getStringOption_("out"); - String out_csv = getStringOption_("out_tsv"); + String out_tsv = getStringOption_("out_tsv"); fast_scoring_ = getStringOption_("RNPxl:scoring") == "fast" ? true : false; @@ -4591,6 +4593,23 @@ static void scoreXLIons_( IDFilter::keepNBestHits(peptide_ids, 1); IDFilter::removeUnreferencedProteins(protein_ids, peptide_ids); + // annotate RNPxl related information to hits and create report + vector csv_rows_percolator = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); + + // save report + if (!out_tsv.empty()) + { + TextFile csv_file; + csv_file.addLine(RNPxlReportRowHeader().getString("\t")); + for (const RNPxlReportRow r : csv_rows_percolator) + { + csv_file.addLine(r.getString("\t")); + } + const String out_percolator_tsv = File::removeExtension(out_tsv) + "_perc.tsv"; + csv_file.store(out_percolator_tsv); + } + + // split PSMs into XLs and non-XLs but keep only best one of both vector pep_pi; vector xl_pi; @@ -4654,7 +4673,7 @@ static void scoreXLIons_( } // save report - if (!out_csv.empty()) + if (!out_tsv.empty()) { TextFile csv_file; csv_file.addLine(RNPxlReportRowHeader().getString("\t")); @@ -4662,7 +4681,7 @@ static void scoreXLIons_( { csv_file.addLine(csv_rows[i].getString("\t")); } - csv_file.store(out_csv); + csv_file.store(out_tsv); } #ifdef _OPENMP From 1a837f87316a93521d4a18a49433274cd79430aa Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 30 Sep 2019 15:33:47 +0200 Subject: [PATCH 078/471] TP FP fast p 324 6 fast 235 3 slow p 314 4 slow 195 0 --- src/utils/OpenNuXL.cpp | 189 ++++++++++++++++++++++++++--------------- 1 file changed, 119 insertions(+), 70 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index a9618468210..33b3515c66f 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -83,6 +83,9 @@ #include #include +#include +#include + #include #include #include @@ -3055,75 +3058,6 @@ static void scoreXLIons_( << "nr_candidates" << "NuXL:rank_product" << "NuXL:wTop50"; -#ifdef OPENNUXL_SEPARATE_FEATURES - for (auto & pi : peptide_ids) - { - for (auto & ph : pi.getHits()) - { - if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) - { - ph.setMetaValue("XL_NuXL:mass_error_p", 0.0); - ph.setMetaValue("XL_NuXL:err", 0.0); - ph.setMetaValue("XL_NuXL:total_loss_score",0.0); - ph.setMetaValue("XL_NuXL:modds", 0.0); - ph.setMetaValue("XL_NuXL:immonium_score", 0.0); - ph.setMetaValue("XL_NuXL:precursor_score", 0.0); - ph.setMetaValue("XL_NuXL:MIC", 0.0); - ph.setMetaValue("XL_NuXL:Morph", 0.0); - ph.setMetaValue("XL_NuXL:total_MIC", 0.0); - ph.setMetaValue("XL_NuXL:ladder_score", 0.0); - ph.setMetaValue("XL_NuXL:sequence_score", 0.0); - ph.setMetaValue("XL_NuXL:total_Morph", 0.0); - ph.setMetaValue("XL_NuXL:total_HS", 0.0); - } - else // XL - { - ph.setMetaValue("XL_NuXL:mass_error_p", static_cast(ph.getMetaValue("NuXL:mass_error_p"))); - ph.setMetaValue("XL_NuXL:err", static_cast(ph.getMetaValue("NuXL:err"))); - ph.setMetaValue("XL_NuXL:total_loss_score", static_cast(ph.getMetaValue("NuXL:total_loss_score"))); - ph.setMetaValue("XL_NuXL:modds", static_cast(ph.getMetaValue( "NuXL:modds"))); - ph.setMetaValue("XL_NuXL:immonium_score", static_cast(ph.getMetaValue("NuXL:immonium_score"))); - ph.setMetaValue("XL_NuXL:precursor_score", static_cast(ph.getMetaValue("NuXL:precursor_score"))); - ph.setMetaValue("XL_NuXL:MIC", static_cast(ph.getMetaValue("NuXL:MIC"))); - ph.setMetaValue("XL_NuXL:Morph", static_cast(ph.getMetaValue("NuXL:Morph"))); - ph.setMetaValue("XL_NuXL:total_MIC", static_cast(ph.getMetaValue( "NuXL:total_MIC"))); - ph.setMetaValue("XL_NuXL:ladder_score", static_cast(ph.getMetaValue("NuXL:ladder_score"))); - ph.setMetaValue("XL_NuXL:sequence_score", static_cast(ph.getMetaValue("NuXL:sequence_score"))); - ph.setMetaValue("XL_NuXL:total_Morph", static_cast(ph.getMetaValue("NuXL:total_Morph"))); - ph.setMetaValue("XL_NuXL:total_HS", static_cast(ph.getMetaValue("NuXL:total_HS"))); - - ph.setMetaValue("NuXL:mass_error_p", 0.0); - ph.setMetaValue("NuXL:err", 0.0); - ph.setMetaValue("NuXL:total_loss_score",0.0); - ph.setMetaValue("NuXL:modds", 0.0); - ph.setMetaValue("NuXL:immonium_score", 0.0); - ph.setMetaValue("NuXL:precursor_score", 0.0); - ph.setMetaValue("NuXL:MIC", 0.0); - ph.setMetaValue("NuXL:Morph", 0.0); - ph.setMetaValue("NuXL:total_MIC", 0.0); - ph.setMetaValue("NuXL:ladder_score", 0.0); - ph.setMetaValue("NuXL:sequence_score", 0.0); - ph.setMetaValue("NuXL:total_Morph", 0.0); - ph.setMetaValue("NuXL:total_HS", 0.0); - } - } - } - - feature_set - << "XL_NuXL:mass_error_p" - << "XL_NuXL:err" - << "XL_NuXL:total_loss_score" - << "XL_NuXL:modds" - << "XL_NuXL:immonium_score" - << "XL_NuXL:precursor_score" - << "XL_NuXL:MIC" - << "XL_NuXL:Morph" - << "XL_NuXL:total_MIC" - << "XL_NuXL:ladder_score" - << "XL_NuXL:sequence_score" - << "XL_NuXL:total_Morph" - << "XL_NuXL:total_HS"; -#endif feature_set << "NuXL:marker_ions_score" @@ -3145,6 +3079,41 @@ static void scoreXLIons_( << "NuXL:NA_MASS_z0" << "NuXL:NA_length" << "nucleotide_mass_tags"; + +#ifdef OPENNUXL_SEPARATE_FEATURES + for (auto & pi : peptide_ids) + { + for (auto & ph : pi.getHits()) + { + if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) + { + // fill XL related feature columns with zeros + for (auto s : feature_set) + { + if (s.hasPrefix("NuXL") ph.setMetaValue("XL_" + s, 0.0); + } + } + else // XL + { + // fill linear peptide releated feature columns with zero (after copying them over) + for (auto s : feature_set) + { + if (s.hasPrefix("NuXL") + { + ph.setMetaValue("XL_" + s, static_cast(ph.getMetaValue(s))); + ph.setMetaValue(s, 0.0); + } + } + } + } + } + + // we duplicated the feature set + auto XL_columns = feature_set; + for (auto s : feature_set) { if (s.hasPrefix("NuXL") XL_columns.push_back("XL_" + s); } + feature_set = XL_columns; +#endif + #ifdef DANGEROUS_FEAUTURES feature_set << "CountSequenceIsTop" @@ -4499,7 +4468,87 @@ static void scoreXLIons_( map_index2ppm.clear(); if (generate_decoys) - { + { + // calculate tail median score of decoys for specific meta value + auto metaMedian = [](const vector & peptide_ids, const String name)->double + { + vector decoy_XL_scores; + for (const auto & pi : peptide_ids) + { + for (const auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + if (!is_XL || ph.getMetaValue("target_decoy") != "decoy") continue; + double score = ph.getMetaValue(name); + decoy_XL_scores.push_back(score); + } + } + std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); + decoy_XL_scores.resize(1000); + return Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); + }; + + /* + // calibrate scores by tail of decoy distribution + vector decoy_XL_scores; + vector decoy_peptide_scores; + for (const auto & pi : peptide_ids) + { + for (const auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + if (ph.getMetaValue("target_decoy") != "decoy") continue; + double score = ph.getScore(); + if (is_XL) { decoy_XL_scores.push_back(score); } + else { decoy_peptide_scores.push_back(score); } + } + } + std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); + std::sort(decoy_peptide_scores.begin(), decoy_peptide_scores.end(), greater()); + decoy_XL_scores.resize(1000); + decoy_peptide_scores.resize(1000); + double mxl = Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); + double mpep = Math::median(decoy_peptide_scores.begin(), decoy_peptide_scores.end()); + double diff = mpep - mxl; + cout << "Difference between medians of decoy distributions (tails pep-XL): " << diff << endl; + for (auto & pi : peptide_ids) + { + for (auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + double score = ph.getScore(); + //if (is_XL) { ph.setScore(score + diff); } // equalize medians of tails + if (!is_XL) + { + ph.setMetaValue(); // impute missing with medians + } + } + pi.assignRanks(); + } +*/ + map medians; + for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) + { + medians[mn] = metaMedian(peptide_ids, mn); + } + + for (auto & pi : peptide_ids) + { + for (auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + double score = ph.getScore(); + //if (is_XL) { ph.setScore(score + diff); } // equalize medians of tails + if (!is_XL) + { + for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) + { + ph.setMetaValue(mn, medians[mn]); // impute missing with medians + } + } + } + pi.assignRanks(); + } fdr.apply(peptide_ids); // write ProteinIdentifications and PeptideIdentifications to IdXML From 72183ddae6a0e0268eb0a9b4d2f973d2479dd70d Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 30 Sep 2019 15:54:15 +0200 Subject: [PATCH 079/471] enabled separate features --- src/utils/OpenNuXL.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 33b3515c66f..22dc057cb06 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -106,6 +106,8 @@ #endif //#define DEBUG_OpenNuXL 1 +//#define OPENNUXL_SEPARATE_FEATURES 1 +#define DANGEROUS_FEAUTURES using namespace OpenMS; using namespace OpenMS::Internal; @@ -3090,7 +3092,7 @@ static void scoreXLIons_( // fill XL related feature columns with zeros for (auto s : feature_set) { - if (s.hasPrefix("NuXL") ph.setMetaValue("XL_" + s, 0.0); + if (s.hasPrefix("NuXL")) ph.setMetaValue("XL_" + s, 0.0); } } else // XL @@ -3098,7 +3100,7 @@ static void scoreXLIons_( // fill linear peptide releated feature columns with zero (after copying them over) for (auto s : feature_set) { - if (s.hasPrefix("NuXL") + if (s.hasPrefix("NuXL")) { ph.setMetaValue("XL_" + s, static_cast(ph.getMetaValue(s))); ph.setMetaValue(s, 0.0); @@ -3110,7 +3112,7 @@ static void scoreXLIons_( // we duplicated the feature set auto XL_columns = feature_set; - for (auto s : feature_set) { if (s.hasPrefix("NuXL") XL_columns.push_back("XL_" + s); } + for (auto s : feature_set) { if (s.hasPrefix("NuXL")) XL_columns.push_back("XL_" + s); } feature_set = XL_columns; #endif From 1619a70e3c10f32296b9862b522c5bc476e122c8 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 1 Oct 2019 12:58:28 +0200 Subject: [PATCH 080/471] disabled dangerous features --- src/utils/OpenNuXL.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 22dc057cb06..8121b428059 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -107,7 +107,7 @@ //#define DEBUG_OpenNuXL 1 //#define OPENNUXL_SEPARATE_FEATURES 1 -#define DANGEROUS_FEAUTURES +//#define DANGEROUS_FEAUTURES increases FDR on entrappment dataset using namespace OpenMS; using namespace OpenMS::Internal; From 8a665912d6ed5903be24b10eae210a1df925c54e Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 10 Oct 2019 14:12:14 +0200 Subject: [PATCH 081/471] removed all filters for best results... --- src/utils/OpenNuXL.cpp | 227 ++++++++++++++++++++++++++++------------- 1 file changed, 158 insertions(+), 69 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 8121b428059..1abe659242f 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -108,6 +108,10 @@ //#define DEBUG_OpenNuXL 1 //#define OPENNUXL_SEPARATE_FEATURES 1 //#define DANGEROUS_FEAUTURES increases FDR on entrappment dataset +//#define FILTER_BAD_PARTIAL_LOSS_SCORES filters out some good (difficult) hits but decreases overall false positives +//#define FILTER_BAD_SCORES_ID_TAGS filter out some good hits +//#define FILTER_AMBIGIOUS_PEAKS +//#define FILTER_NO_ARBITRARY_TAG_PRESENT using namespace OpenMS; using namespace OpenMS::Internal; @@ -939,6 +943,21 @@ class OpenNuXL : OPENMS_PRECONDITION(partial_loss_template_z1_b_ions.size() == partial_loss_template_z1_y_ions.size(), "b- and y-ion arrays must have same size."); OPENMS_PRECONDITION(partial_loss_template_z1_b_ions.size() > 0, "b- and y-ion arrays must not be empty."); +#ifdef FILTER_AMBIGIOUS_PEAKS + // is the mass shift ambigious and common in non-XL data (e.g.: freq > 10%) + auto ambigious_match = [&](const double& previous_theo_mass, const double& current_theo_mass)->bool + { + const double dist = current_theo_mass - previous_theo_mass; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? current_theo_mass * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + auto low_it = mass2high_frequency_.lower_bound(dist - max_dist_dalton); + if (low_it != mass2high_frequency_.end() && fabs(low_it->first - dist) < max_dist_dalton) // in tolerance window? + { + return true; // ambigious match + } + return false; + }; +#endif + double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 @@ -956,6 +975,7 @@ class OpenNuXL : { const double theo_mz = (partial_loss_template_z1_b_ions[i] + fa.mass + diff2b + (z-1) * Constants::PROTON_MASS_U) / z; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak @@ -969,6 +989,14 @@ class OpenNuXL : { if (!peak_matched[index]) { +#ifdef FILTER_AMBIGIOUS_PEAKS + // skip ambigious matches + if (i >= 1) + { + if (ambigious_match(partial_loss_template_z1_b_ions[i - 1], partial_loss_template_z1_b_ions[i] + fa.mass)) continue; + } +#endif + const double intensity = exp_spectrum[index].getIntensity(); b_mean_err += intensity * std::abs(theo_mz - exp_mz); dot_product += intensity; @@ -990,6 +1018,7 @@ class OpenNuXL : { const double theo_mz = (partial_loss_template_z1_y_ions[i] + fa.mass + (z-1) * Constants::PROTON_MASS_U) / z; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak @@ -1003,6 +1032,14 @@ class OpenNuXL : { if (!peak_matched[index]) { +#ifdef FILTER_AMBIGIOUS_PEAKS + // skip ambigious matches + if (i >= 1) + { + if (ambigious_match(partial_loss_template_z1_y_ions[i - 1], partial_loss_template_z1_y_ions[i] + fa.mass)) continue; + } +#endif + const double intensity = exp_spectrum[index].getIntensity(); y_mean_err += intensity * std::abs(theo_mz - exp_mz); dot_product += intensity; @@ -1519,6 +1556,7 @@ static void scoreXLIons_( } }; + RankScores rankScores_(const MSSpectrum& spectrum, vector peak_matched) { double matched = std::accumulate(peak_matched.begin(), peak_matched.end(), 0); @@ -1550,6 +1588,10 @@ static void scoreXLIons_( return r; } +#ifdef FILTER_AMBIGIOUS_PEAKS + static map mass2high_frequency_; +#endif + void calculateNucleotideTags_(PeakMap& exp, const double fragment_mass_tolerance, const bool fragment_mass_tolerance_unit_ppm, @@ -1567,14 +1609,17 @@ static void scoreXLIons_( // mass shift to residue + adduct (including no adduct) map > aa_plus_adduct_mass; - auto residues = ResidueDB::getInstance()->getResidues("Natural20"); + auto residues = ResidueDB::getInstance()->getResidues("Natural19WithoutI"); for (const double d : adduct_mass) { for (const Residue* r : residues) { double m = d + r->getMonoWeight(Residue::Internal); - if (aa_plus_adduct_mass.count(m) > 0) cout << "WARNING: mass " << m << " of residue " << r->getName() << " with adduct " << d << " already present." << endl; + if (aa_plus_adduct_mass.count(m) > 0) + { + cout << "WARNING: mass " << m << " of residue " << r->getName() << " with adduct " << d << " already present with " << aa_plus_adduct_mass[m].first->getName() << " and adduct " << aa_plus_adduct_mass[m].second << endl; + } aa_plus_adduct_mass[m] = {r, d}; } } @@ -1582,7 +1627,10 @@ static void scoreXLIons_( for (const Residue* r : residues) { double m = r->getMonoWeight(Residue::Internal); - if (aa_plus_adduct_mass.count(m) > 0) cout << "WARNING: mass " << m << " of residue " << r->getName() << " already present." << endl; + if (aa_plus_adduct_mass.count(m) > 0) + { + cout << "WARNING: mass " << m << " of residue " << r->getName() << " already present with " << aa_plus_adduct_mass[m].first->getName() << " and adduct " << aa_plus_adduct_mass[m].second << endl; + } aa_plus_adduct_mass[m] = {r, 0}; } @@ -1600,11 +1648,13 @@ static void scoreXLIons_( size_t match(0); size_t in_mass_range(0); + + // for all peak pairs for (Size i = 0; i != mzs.size(); ++i) { for (Size j = i+1; j < mzs.size(); ++j) { - double m = mzs[j]; + double m = mzs[j]; double dm = m - mzs[i]; if (charges[i] != charges[j]) continue; @@ -1613,6 +1663,7 @@ static void scoreXLIons_( auto left = adduct_mass.lower_bound((dm * charges[i]) - tolerance); if (left == adduct_mass.end()) continue; ++in_mass_range; + // count if distance matches to adduct mass if (fabs(*left - (dm * charges[i])) < tolerance ) { ++match; @@ -1671,17 +1722,16 @@ static void scoreXLIons_( spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = tagger.getLongestTag(spec).size(); spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].setName("longest_tag"); } -/* + + + // Calculate background statistics on shifts for (const auto& mra : aa_plus_adduct_mass) { double m = mra.first; const pair& residue_adduct = mra.second; - cout << m << "\t" << residue_adduct.first->getOneLetterCode() << "\ŧ" << residue_adduct.second << endl; + cout << m << "\t" << residue_adduct.first->getOneLetterCode() << "\t" << residue_adduct.second << endl; } -*/ - -/* cout << "Distinct residue + adduct pairs: " << aa_plus_adduct_mass_count.size() << endl; map > aa2mass2count; @@ -1693,14 +1743,31 @@ static void scoreXLIons_( String name = residue->getName(); aa2mass2count[residue][mc.first] = mc.second; } + cout << "Total counts per residue:" << endl; + +#ifdef FILTER_AMBIGIOUS_PEAKS + mass2high_frequency_.clear(); +#endif for (const auto& aa2 : aa2mass2count) { - for (const auto m2c : aa2.second) + auto& mass2count = aa2.second; + for (const auto m2c : mass2count) { + // counts cout << aa2.first->getName() << "\t" << m2c.first << "\t" << m2c.second << endl; // aa mass count + // frequency + double frequency_normalized = (double)m2c.second / mass2count.begin()->second; + +#ifdef FILTER_AMBIGIOUS_PEAKS + if (frequency_normalized > 0.5 && frequency_normalized != 1.0) // residue with shift (=freq. is different to 1) + { + mass2high_frequency_[m2c.first] = frequency_normalized; + } +#endif } } + cout << "Normalized counts per residue:" << endl; for (const auto& aa2 : aa2mass2count) { @@ -1708,11 +1775,18 @@ static void scoreXLIons_( for (const auto m2c : mass2count) { // normalize by counts - cout << aa2.first->getName() << "\t" << m2c.first << "\t" << (double)m2c.second / mass2count.begin()->second << endl ; // aa mass count + double frequency_normalized = (double)m2c.second / mass2count.begin()->second; + cout << aa2.first->getName() << "\t" << m2c.first << "\t" << frequency_normalized << endl ; // aa mass count } } -*/ +#ifdef FILTER_AMBIGIOUS_PEAKS + cout << "Frequent background mass shifts (mass vs. freq):" << endl; + for (auto & hf : mass2high_frequency_) + { + cout << hf.first << "\t" << hf.second << endl; + } +#endif } /* @brief Filter spectra to remove noise. @@ -1731,7 +1805,7 @@ static void scoreXLIons_( double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, - bool annotate_charge = false) + bool annotate_charge) { // filter MS2 map // remove 0 intensities @@ -1768,7 +1842,8 @@ static void scoreXLIons_( // deisotope Deisotoper::deisotopeAndSingleCharge(spec, - fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, + 0.05, + false, 1, 3, false, 2, 10, @@ -3701,12 +3776,11 @@ static void scoreXLIons_( progresslogger.startProgress(0, 1, "Filtering spectra..."); const bool convert_to_single_charge = false; // whether to convert fragment peaks with isotopic patterns to single charge - const bool annotate_charge = true; preprocessSpectra_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, convert_to_single_charge, - annotate_charge); + true); // annotate charge progresslogger.endProgress(); calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); @@ -3920,8 +3994,10 @@ static void scoreXLIons_( const Size & scan_index = l->second.first; const PeakSpectrum & exp_spectrum = spectra[scan_index]; +#ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } +#endif // count candidate for spectrum #ifdef _OPENMP @@ -4006,10 +4082,11 @@ static void scoreXLIons_( ah.rank_product = rankscores.rp; ah.wTop50 = rankscores.wTop50; + // do we have at least one ladder peak const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, vector()); - +#ifdef FILTER_BAD_SCORES_ID_TAGS if (longest_tags.tag_unshifted == 0) continue; - +#endif ah.tag_XLed = longest_tags.tag_XLed; ah.tag_unshifted = longest_tags.tag_unshifted; ah.tag_shifted = longest_tags.tag_shifted; @@ -4087,8 +4164,11 @@ static void scoreXLIons_( { const Size & scan_index = l->second.first; const PeakSpectrum & exp_spectrum = spectra[scan_index]; +#ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } +#endif + #ifdef _OPENMP omp_set_lock(&(annotated_peptides_lock[scan_index])); omp_set_lock(&(annotated_XLs_lock[scan_index])); @@ -4177,12 +4257,13 @@ static void scoreXLIons_( const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC + marker_ions_sub_score; +#ifdef FILTER_BAD_PARTIAL_LOSS_SCORES // decreases number of hits (especially difficult cases - but also number of false discoveries) if (badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, plss_pc_MIC, marker_ions_sub_score)) { continue; } - +#endif const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); @@ -4233,18 +4314,20 @@ static void scoreXLIons_( ah.sequence_score = ladderScore_(range) / (double)intensity_linear.size(); } - const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, intensity_xls); RankScores rankscores = rankScores_(exp_spectrum, peak_matched); ah.rank_product = rankscores.rp; ah.wTop50 = rankscores.wTop50; - ah.tag_XLed = longest_tags.tag_XLed; - ah.tag_unshifted = longest_tags.tag_unshifted; - ah.tag_shifted = longest_tags.tag_shifted; // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one + const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, intensity_xls); +#ifdef FILTER_BAD_SCORES_ID_TAGS if (longest_tags.tag_XLed == 0) { continue; } +#endif + ah.tag_XLed = longest_tags.tag_XLed; + ah.tag_unshifted = longest_tags.tag_unshifted; + ah.tag_shifted = longest_tags.tag_shifted; // combined score const double tags = exp_spectrum.getFloatDataArrays()[1][0]; @@ -4279,12 +4362,16 @@ static void scoreXLIons_( for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; +#ifdef FILTER_NO_ARBITRARY_TAG_PRESENT + // require at least one mass tag + if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } +#endif #ifdef _OPENMP - omp_set_lock(&(annotated_peptides_lock[scan_index])); - omp_set_lock(&(annotated_XLs_lock[scan_index])); - ++nr_candidates[scan_index]; - omp_unset_lock(&(annotated_XLs_lock[scan_index])); - omp_unset_lock(&(annotated_peptides_lock[scan_index])); + omp_set_lock(&(annotated_peptides_lock[scan_index])); + omp_set_lock(&(annotated_XLs_lock[scan_index])); + ++nr_candidates[scan_index]; + omp_unset_lock(&(annotated_XLs_lock[scan_index])); + omp_unset_lock(&(annotated_peptides_lock[scan_index])); #endif const int & isotope_error = l->second.second; const double & exp_pc_mass = l->first; @@ -4471,27 +4558,49 @@ static void scoreXLIons_( if (generate_decoys) { - // calculate tail median score of decoys for specific meta value - auto metaMedian = [](const vector & peptide_ids, const String name)->double - { - vector decoy_XL_scores; - for (const auto & pi : peptide_ids) + + // calculate median score of decoys for specific meta value + auto metaMedian = [](const vector & peptide_ids, const String name)->double { - for (const auto & ph : pi.getHits()) + vector decoy_XL_scores; + for (const auto & pi : peptide_ids) { - const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - if (!is_XL || ph.getMetaValue("target_decoy") != "decoy") continue; - double score = ph.getMetaValue(name); - decoy_XL_scores.push_back(score); + for (const auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + if (!is_XL || ph.getMetaValue("target_decoy") != "decoy") continue; + double score = ph.getMetaValue(name); + decoy_XL_scores.push_back(score); + } } + std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); + return Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); + }; + + map medians; + for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) + { + medians[mn] = metaMedian(peptide_ids, mn); } - std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); - decoy_XL_scores.resize(1000); - return Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); - }; - /* - // calibrate scores by tail of decoy distribution + for (auto & pi : peptide_ids) + { + for (auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + double score = ph.getScore(); + if (!is_XL) + { + for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) + { + ph.setMetaValue(mn, medians[mn]); // impute missing with medians + } + } + } + pi.assignRanks(); + } +/* + // calibrate scores by decoy distribution vector decoy_XL_scores; vector decoy_peptide_scores; for (const auto & pi : peptide_ids) @@ -4507,8 +4616,6 @@ static void scoreXLIons_( } std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); std::sort(decoy_peptide_scores.begin(), decoy_peptide_scores.end(), greater()); - decoy_XL_scores.resize(1000); - decoy_peptide_scores.resize(1000); double mxl = Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); double mpep = Math::median(decoy_peptide_scores.begin(), decoy_peptide_scores.end()); double diff = mpep - mxl; @@ -4527,30 +4634,8 @@ static void scoreXLIons_( } pi.assignRanks(); } -*/ - map medians; - for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) - { - medians[mn] = metaMedian(peptide_ids, mn); - } +*/ - for (auto & pi : peptide_ids) - { - for (auto & ph : pi.getHits()) - { - const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - double score = ph.getScore(); - //if (is_XL) { ph.setScore(score + diff); } // equalize medians of tails - if (!is_XL) - { - for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) - { - ph.setMetaValue(mn, medians[mn]); // impute missing with medians - } - } - } - pi.assignRanks(); - } fdr.apply(peptide_ids); // write ProteinIdentifications and PeptideIdentifications to IdXML @@ -4815,6 +4900,10 @@ static void scoreXLIons_( } }; +#ifdef FILTER_AMBIGIOUS_PEAKS +map OpenNuXL::mass2high_frequency_ = {}; +#endif + int main(int argc, const char** argv) { OpenNuXL tool; From 03b80657fb8f2556637d1f1e0420ddefa8686508 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 15 Oct 2019 10:34:52 +0200 Subject: [PATCH 082/471] enable disable ppm filtering by command line option --- src/utils/OpenNuXL.cpp | 293 ++++++++++++++++++++--------------------- 1 file changed, 146 insertions(+), 147 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1abe659242f..14c88d4f072 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -108,9 +108,8 @@ //#define DEBUG_OpenNuXL 1 //#define OPENNUXL_SEPARATE_FEATURES 1 //#define DANGEROUS_FEAUTURES increases FDR on entrappment dataset -//#define FILTER_BAD_PARTIAL_LOSS_SCORES filters out some good (difficult) hits but decreases overall false positives //#define FILTER_BAD_SCORES_ID_TAGS filter out some good hits -//#define FILTER_AMBIGIOUS_PEAKS +//#define FILTER_AMBIGIOUS_PEAKS //#define FILTER_NO_ARBITRARY_TAG_PRESENT using namespace OpenMS; @@ -537,6 +536,9 @@ class OpenNuXL : registerDoubleOption_("RNPxl:filter_small_peptide_mass", "", 600.0, "Filter precursor that can only correspond to non-crosslinks by mass.", false, true); registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); + + registerStringList_("filter", "", {"filter_pc_mass_error", "impute_decoy_medians"}, "Filtering steps applied to results.", false, true); + setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores"}); } @@ -996,7 +998,6 @@ class OpenNuXL : if (ambigious_match(partial_loss_template_z1_b_ions[i - 1], partial_loss_template_z1_b_ions[i] + fa.mass)) continue; } #endif - const double intensity = exp_spectrum[index].getIntensity(); b_mean_err += intensity * std::abs(theo_mz - exp_mz); dot_product += intensity; @@ -1039,7 +1040,6 @@ class OpenNuXL : if (ambigious_match(partial_loss_template_z1_y_ions[i - 1], partial_loss_template_z1_y_ions[i] + fa.mass)) continue; } #endif - const double intensity = exp_spectrum[index].getIntensity(); y_mean_err += intensity * std::abs(theo_mz - exp_mz); dot_product += intensity; @@ -1288,14 +1288,17 @@ score += ah.mass_error_p * 1.15386068 + isXL * 3.0 * ah.marker_ions_score + 3.0 * ah.total_MIC + ah.ladder_score; */ + return 10.0 * ah.total_loss_score - + 0.1 * ah.mass_error_p + + 1.0 * ah.partial_loss_score + + 0.1 * ah.mass_error_p - 10.0 * ah.err - 10.0 * ah.pl_err - + 3.0 * ah.pl_MIC + + 3.0 * ah.pl_MIC + isXL * 3.0 * ah.marker_ions_score - + 3.0 * ah.total_MIC + ah.ladder_score; + + 3.0 * ah.total_MIC + + 1.0 * ah.ladder_score; /* -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err @@ -1608,7 +1611,7 @@ static void scoreXLIons_( } // mass shift to residue + adduct (including no adduct) - map > aa_plus_adduct_mass; + map > aa_plus_adduct_mass; auto residues = ResidueDB::getInstance()->getResidues("Natural19WithoutI"); for (const double d : adduct_mass) @@ -1616,23 +1619,29 @@ static void scoreXLIons_( for (const Residue* r : residues) { double m = d + r->getMonoWeight(Residue::Internal); - if (aa_plus_adduct_mass.count(m) > 0) - { - cout << "WARNING: mass " << m << " of residue " << r->getName() << " with adduct " << d << " already present with " << aa_plus_adduct_mass[m].first->getName() << " and adduct " << aa_plus_adduct_mass[m].second << endl; - } - aa_plus_adduct_mass[m] = {r, d}; + aa_plus_adduct_mass[m][r] = d; // mass, residue, shift mass } } // add mass shits of plain residues for (const Residue* r : residues) { double m = r->getMonoWeight(Residue::Internal); - if (aa_plus_adduct_mass.count(m) > 0) + aa_plus_adduct_mass[m][r] = 0; + } + + // output ambigious masses + cout << "Ambigious residues (+adduct) masses that exactly match to other masses." << endl; + cout << "Total\tResidue\tAdduct" << endl; + for (auto& m : aa_plus_adduct_mass) + { + double mass = m.first; + if (m.second.size() == 1) continue; // more than one residue / adduct registered for that mass + for (auto& a : m.second) { - cout << "WARNING: mass " << m << " of residue " << r->getName() << " already present with " << aa_plus_adduct_mass[m].first->getName() << " and adduct " << aa_plus_adduct_mass[m].second << endl; + cout << mass << "\t" << a.first->getOneLetterCode() << "\t+\t" << a.second << endl; } - aa_plus_adduct_mass[m] = {r, 0}; - } + } + map adduct_mass_count; map aa_plus_adduct_mass_count; @@ -1672,7 +1681,7 @@ static void scoreXLIons_( } } - size_t aa_plus_adduct_match(0); + // count how often a shift matches a residue + adduct mass (including mass 0 for unmodified residue) size_t aa_plus_adduct_in_mass_range(0); for (Size i = 0; i != mzs.size(); ++i) { @@ -1684,13 +1693,17 @@ static void scoreXLIons_( if (charges[i] != charges[j]) continue; const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, m) : fragment_mass_tolerance; + + // find all (shifted/normal) residues that match to an observed shift auto left = aa_plus_adduct_mass.lower_bound((dm * charges[i]) - tolerance); - if (left == aa_plus_adduct_mass.end()) continue; - ++aa_plus_adduct_in_mass_range; - if (fabs(left->first - (dm * charges[i])) < tolerance ) + auto right = aa_plus_adduct_mass.upper_bound((dm * charges[i]) + tolerance); + for (; left != right; ++left) { - ++aa_plus_adduct_match; - ++aa_plus_adduct_mass_count[left->first]; + ++aa_plus_adduct_in_mass_range; + if (fabs(left->first - (dm * charges[i])) < tolerance ) + { + ++aa_plus_adduct_mass_count[left->first]; + } } } } @@ -1723,25 +1736,36 @@ static void scoreXLIons_( spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].setName("longest_tag"); } - + cout << "Distinct residue + adduct masses (including residues without shift): " << aa_plus_adduct_mass_count.size() << endl; // Calculate background statistics on shifts + cout << "mass\tresidue\tshift:" << endl; for (const auto& mra : aa_plus_adduct_mass) { double m = mra.first; - const pair& residue_adduct = mra.second; - cout << m << "\t" << residue_adduct.first->getOneLetterCode() << "\t" << residue_adduct.second << endl; + const map& residue2adduct = mra.second; + for (auto& r2a : residue2adduct) + { + cout << m << "\t" << r2a.first->getOneLetterCode() << "\t" << r2a.second << endl; + } } - cout << "Distinct residue + adduct pairs: " << aa_plus_adduct_mass_count.size() << endl; + // reformat to get: amino acid, mass, count statistics map > aa2mass2count; - for (const auto& mc : aa_plus_adduct_mass_count) { - auto it = aa_plus_adduct_mass.lower_bound(mc.first - 1e-6); + double mass = mc.first; + size_t count = mc.second; + + auto it = aa_plus_adduct_mass.lower_bound(mass - 1e-6); // "exact" match if (it == aa_plus_adduct_mass.end()) continue; - const Residue* residue = it->second.first; - String name = residue->getName(); - aa2mass2count[residue][mc.first] = mc.second; + + const map& residue2adduct = it->second; + for (auto& r2a : residue2adduct) + { + const Residue* residue = r2a.first; + String name = residue->getName(); + aa2mass2count[residue][mass] = count; + } } cout << "Total counts per residue:" << endl; @@ -1754,13 +1778,14 @@ static void scoreXLIons_( auto& mass2count = aa2.second; for (const auto m2c : mass2count) { - // counts - cout << aa2.first->getName() << "\t" << m2c.first << "\t" << m2c.second << endl; // aa mass count - // frequency - double frequency_normalized = (double)m2c.second / mass2count.begin()->second; + double current_mass = m2c.first; + size_t current_residue_count = m2c.second; + size_t unmodified_residue_count = mass2count.begin()->second; + cout << aa2.first->getName() << "\t" << current_mass << "\t" << current_residue_count << endl; // aa, mass, count + double frequency_normalized = (double)current_residue_count / unmodified_residue_count; // frequency relative to unmodified residue #ifdef FILTER_AMBIGIOUS_PEAKS - if (frequency_normalized > 0.5 && frequency_normalized != 1.0) // residue with shift (=freq. is different to 1) + if (frequency_normalized > 0.5 && frequency_normalized != 1.0) // residue with shift as frequent as unmodified residue { mass2high_frequency_[m2c.first] = frequency_normalized; } @@ -1775,8 +1800,11 @@ static void scoreXLIons_( for (const auto m2c : mass2count) { // normalize by counts - double frequency_normalized = (double)m2c.second / mass2count.begin()->second; - cout << aa2.first->getName() << "\t" << m2c.first << "\t" << frequency_normalized << endl ; // aa mass count + double current_mass = m2c.first; + size_t current_residue_count = m2c.second; + size_t unmodified_residue_count = mass2count.begin()->second; + double frequency_normalized = (double)current_residue_count / unmodified_residue_count; + cout << aa2.first->getName() << "\t" << current_mass << "\t" << frequency_normalized << endl ; // aa mass count } } @@ -1787,6 +1815,7 @@ static void scoreXLIons_( cout << hf.first << "\t" << hf.second << endl; } #endif + } /* @brief Filter spectra to remove noise. @@ -3709,6 +3738,11 @@ static void scoreXLIons_( bool cysteine_adduct = getFlag_("RNPxl:CysteineAdduct"); + StringList filter = getStringList_("filter"); + bool filter_pc_mass_error = find(filter.begin(), filter.end(), "filter_pc_mass_error") != filter.end(); + bool impute_decoy_medians = find(filter.begin(), filter.end(), "impute_decoy_medians") != filter.end(); + bool filter_bad_partial_loss_scores = find(filter.begin(), filter.end(), "filter_bad_partial_loss_scores") != filter.end(); + // generate mapping from empirical formula to mass and empirical formula to (one or more) precursor adducts RNPxlModificationMassesResult mm; if (max_nucleotide_length != 0) @@ -4257,13 +4291,11 @@ static void scoreXLIons_( const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC + marker_ions_sub_score; -#ifdef FILTER_BAD_PARTIAL_LOSS_SCORES // decreases number of hits (especially difficult cases - but also number of false discoveries) - if (badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, plss_pc_MIC, marker_ions_sub_score)) + if (filter_bad_partial_loss_scores && badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, plss_pc_MIC, marker_ions_sub_score)) { continue; } -#endif const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); @@ -4515,126 +4547,93 @@ static void scoreXLIons_( } } */ - map> map_index2ppm; - size_t i(0); - double mean(0); - for (size_t index = 0; index != peptide_ids.size(); ++index) - { - if (peptide_ids[index].getHits().empty()) continue; - if (peptide_ids[index].getHits()[0].getMetaValue("target_decoy") == "target" - && (double)peptide_ids[index].getHits()[0].getMetaValue("NuXL:total_loss_score") > 15.0) // not too bad score - { - double ppm_error = peptide_ids[index].getHits()[0].getMetaValue(OpenMS::Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM); - map_index2ppm[peptide_ids[index].getHits()[0].getScore()] = ppm_error; - mean += ppm_error; - ++i; - } - } - mean /= i; - double sd(0); - for (auto & m : map_index2ppm) - { - sd += pow(m.second - mean, 2.0); - } - sd = sqrt(1.0/(double)i * sd); - cout << "mean ppm error: " << mean << " sd: " << sd << " 5*sd: " << 5*sd << endl; - - // as we are dealing with a very large search space, filter out all identifications with mass error > 5 *sd - for (size_t index = 0; index != peptide_ids.size(); ++index) - { - vector& phs = peptide_ids[index].getHits(); - if (phs.empty()) continue; - - auto new_end = std::remove_if(phs.begin(), phs.end(), - [&sd, &mean](const PeptideHit & ph) - { - return fabs((double)ph.getMetaValue(Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM)) - fabs(mean) > 5.0*sd; - }); - phs.erase(new_end, phs.end()); - } - IDFilter::removeEmptyIdentifications(peptide_ids); - - map_index2ppm.clear(); - if (generate_decoys) { - - // calculate median score of decoys for specific meta value - auto metaMedian = [](const vector & peptide_ids, const String name)->double + map> map_index2ppm; + size_t i(0); + double mean(0); + for (size_t index = 0; index != peptide_ids.size(); ++index) { - vector decoy_XL_scores; - for (const auto & pi : peptide_ids) - { - for (const auto & ph : pi.getHits()) - { - const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - if (!is_XL || ph.getMetaValue("target_decoy") != "decoy") continue; - double score = ph.getMetaValue(name); - decoy_XL_scores.push_back(score); - } - } - std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); - return Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); - }; - - map medians; - for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) + if (peptide_ids[index].getHits().empty()) continue; + if (peptide_ids[index].getHits()[0].getMetaValue("target_decoy") == "target" + && (double)peptide_ids[index].getHits()[0].getMetaValue("NuXL:total_loss_score") > 15.0) // not too bad score + { + double ppm_error = peptide_ids[index].getHits()[0].getMetaValue(OpenMS::Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM); + map_index2ppm[peptide_ids[index].getHits()[0].getScore()] = ppm_error; + mean += ppm_error; + ++i; + } + } + mean /= i; + double sd(0); + for (auto & m : map_index2ppm) { - medians[mn] = metaMedian(peptide_ids, mn); + sd += pow(m.second - mean, 2.0); } - - for (auto & pi : peptide_ids) + sd = sqrt(1.0/(double)i * sd); + cout << "mean ppm error: " << mean << " sd: " << sd << " 5*sd: " << 5*sd << endl; + + if (filter_pc_mass_error) { - for (auto & ph : pi.getHits()) + // as we are dealing with a very large search space, filter out all PSMs with mass error > 5 *sd + for (size_t index = 0; index != peptide_ids.size(); ++index) { - const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - double score = ph.getScore(); - if (!is_XL) - { - for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) - { - ph.setMetaValue(mn, medians[mn]); // impute missing with medians - } - } + vector& phs = peptide_ids[index].getHits(); + if (phs.empty()) continue; + auto new_end = std::remove_if(phs.begin(), phs.end(), + [&sd, &mean](const PeptideHit & ph) + { + return fabs((double)ph.getMetaValue(Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM)) - fabs(mean) > 5.0*sd; + }); + phs.erase(new_end, phs.end()); } - pi.assignRanks(); + IDFilter::removeEmptyIdentifications(peptide_ids); } -/* - // calibrate scores by decoy distribution - vector decoy_XL_scores; - vector decoy_peptide_scores; - for (const auto & pi : peptide_ids) + map_index2ppm.clear(); + + if (impute_decoy_medians) { - for (const auto & ph : pi.getHits()) + // calculate median score of decoys for specific meta value + auto metaMedian = [](const vector & peptide_ids, const String name)->double + { + vector decoy_XL_scores; + for (const auto & pi : peptide_ids) + { + for (const auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + if (!is_XL || ph.getMetaValue("target_decoy") != "decoy") continue; + double score = ph.getMetaValue(name); + decoy_XL_scores.push_back(score); + } + } + std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); + return Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); + }; + + map medians; + for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) { - const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - if (ph.getMetaValue("target_decoy") != "decoy") continue; - double score = ph.getScore(); - if (is_XL) { decoy_XL_scores.push_back(score); } - else { decoy_peptide_scores.push_back(score); } + medians[mn] = metaMedian(peptide_ids, mn); } - } - std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); - std::sort(decoy_peptide_scores.begin(), decoy_peptide_scores.end(), greater()); - double mxl = Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); - double mpep = Math::median(decoy_peptide_scores.begin(), decoy_peptide_scores.end()); - double diff = mpep - mxl; - cout << "Difference between medians of decoy distributions (tails pep-XL): " << diff << endl; - for (auto & pi : peptide_ids) - { - for (auto & ph : pi.getHits()) + + for (auto & pi : peptide_ids) { - const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - double score = ph.getScore(); - //if (is_XL) { ph.setScore(score + diff); } // equalize medians of tails - if (!is_XL) - { - ph.setMetaValue(); // impute missing with medians - } + for (auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + double score = ph.getScore(); + if (!is_XL) + { + for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) + { + ph.setMetaValue(mn, medians[mn]); // impute missing with medians + } + } + } + pi.assignRanks(); } - pi.assignRanks(); } -*/ fdr.apply(peptide_ids); From de83f493aa9b5bf0ad246295b9213440361d991d Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 25 Oct 2019 12:54:31 +0200 Subject: [PATCH 083/471] SVM score recalibration --- src/utils/OpenNuXL.cpp | 158 +++++++++++++++++++++++++++++++++++++++-- 1 file changed, 154 insertions(+), 4 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 14c88d4f072..1fd3d4d3f65 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -92,8 +92,11 @@ #include +#include + #include #include +#include #include #include @@ -451,7 +454,7 @@ class OpenNuXL : StringList all_enzymes; ProteaseDB::getInstance()->getAllNames(all_enzymes); - registerStringOption_("peptide:enzyme", "", "Trypsin", "The enzyme used for peptide digestion.", false); + registerStringOption_("peptide:enzyme", "", "Trypsin/P", "The enzyme used for peptide digestion.", false); setValidStrings_("peptide:enzyme", all_enzymes); registerTOPPSubsection_("report", "Reporting Options"); @@ -1531,7 +1534,6 @@ static void scoreXLIons_( double wTop50 = 0; }; - class SmallestElements { private: @@ -4622,12 +4624,11 @@ static void scoreXLIons_( for (auto & ph : pi.getHits()) { const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - double score = ph.getScore(); if (!is_XL) { for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) { - ph.setMetaValue(mn, medians[mn]); // impute missing with medians + ph.setMetaValue(mn, medians[mn]); // impute missing with medians } } } @@ -4635,6 +4636,155 @@ static void scoreXLIons_( } } + ///////////////////////////////////////// SVM score recalibration + // find size of minority class + size_t minority_class(0); + map pep_t; + map pep_d; + map XL_t; + map XL_d; + + for (size_t index = 0; index != peptide_ids.size(); ++index) + { + if (peptide_ids[index].getHits().empty()) continue; + const PeptideHit& ph = peptide_ids[index].getHits()[0]; + bool is_target = ph.getMetaValue("target_decoy") == "target"; + bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + if (is_target) + { + if (is_XL) + { + XL_t[ph.getScore()] = index; + } + else + { + pep_t[ph.getScore()] = index; + } + } + else + { + if (is_XL) + { + XL_d[ph.getScore()] = index; + } + else + { + pep_d[ph.getScore()] = index; + } + } + } + minority_class = std::min({pep_t.size(), pep_d.size(), XL_t.size(), XL_d.size()}); + cout << "Peptide (target/decoy)\t XL (target/decoy):" << endl; + cout << pep_t.size() << "\t" << pep_d.size() << "\t" << XL_t.size() << "\t" << XL_d.size() << endl; + + // keep only top elements + auto right = std::next(pep_t.begin(), (long unsigned int)(pep_t.size() - minority_class)); + pep_t.erase(pep_t.begin(), right); + pep_d.erase(pep_d.begin(), std::next(pep_d.begin(), pep_d.size() - minority_class)); + XL_t.erase(XL_t.begin(), next(XL_t.begin(), XL_t.size() - minority_class)); + XL_d.erase(XL_d.begin(), next(XL_d.begin(), XL_d.size() - minority_class)); + + set training_indices; + for (auto & l : {pep_t, pep_d, XL_t, XL_d}) + { + for (auto & i : l) training_indices.insert(i.second); + } + + if (minority_class > 100) + { + SimpleSVM::PredictorMap predictors; + map labels; + + StringList feature_set; + feature_set + << "NuXL:mass_error_p" + << "NuXL:err" + << "NuXL:total_loss_score" + << "NuXL:modds" + << "NuXL:immonium_score" + << "NuXL:precursor_score" + << "NuXL:MIC" + << "NuXL:Morph" + << "NuXL:total_MIC" + << "NuXL:ladder_score" + << "NuXL:sequence_score" + << "NuXL:total_Morph" + << "NuXL:total_HS" + << "NuXL:tag_XLed" + << "NuXL:tag_unshifted" + << "NuXL:tag_shifted" + << "NuXL:aminoacid_max_tag" + << "NuXL:aminoacid_id_to_max_tag_ratio" + << "nr_candidates" + << "NuXL:rank_product" + << "NuXL:wTop50" + << "NuXL:marker_ions_score" + << "NuXL:partial_loss_score" + << "NuXL:pl_MIC" + << "NuXL:pl_err" + << "NuXL:pl_Morph" + << "NuXL:pl_modds" + << "NuXL:pl_pc_MIC" + << "NuXL:pl_im_MIC" + << "NuXL:isPhospho" + << "NuXL:isXL" + << "NuXL:score" + << "isotope_error" + << "variable_modifications" + << "precursor_intensity_log10" + << "NuXL:NA_MASS_z0" + << "NuXL:NA_length" + << "nucleotide_mass_tags"; + + // copy all scores in predictors ("score" + all from feature_set). + // Only add labels for balanced training set + for (size_t index = 0; index != peptide_ids.size(); ++index) + { + const vector& phits = peptide_ids[index].getHits(); + for (size_t psm_rank = 0; psm_rank != phits.size(); ++psm_rank) + { + const PeptideHit& ph = phits[psm_rank]; + bool is_target = ph.getMetaValue("target_decoy") == "target"; + double score = ph.getScore(); + predictors["score"].push_back(score); + predictors["length"].push_back(ph.getSequence().size()); + for (auto & f : feature_set) + { + double value = ph.getMetaValue(f); + predictors[f].push_back(value); + } + // only add label for training data (rank = 0 and previously selected for training) + if (psm_rank == 0 && training_indices.count(index) > 0) + { + labels[predictors["score"].size() - 1] = is_target; + } + } + } + + SimpleSVM svm; + Param svm_param = svm.getParameters(); + svm_param.setValue("log2_C", ListUtils::create("11.0")); + svm_param.setValue("log2_gamma", ListUtils::create("-5.0")); + svm.setParameters(svm_param); + svm.setup(predictors, labels); + vector predictions; + svm.predict(predictions); + + size_t psm_index(0); + for (size_t index = 0; index != peptide_ids.size(); ++index) + { + vector& phits = peptide_ids[index].getHits(); + for (size_t psm_rank = 0; psm_rank != phits.size(); ++psm_rank, ++psm_index) + { + PeptideHit& ph = phits[psm_rank]; + ph.setScore(predictions[psm_index].probabilities[1]); // set probability of being a target as score + } + peptide_ids[index].assignRanks(); + } +#ifdef DEBUG_OpenNuXL + IdXMLFile().store(out_idxml + "_svm.idXML", protein_ids, peptide_ids); +#endif + } fdr.apply(peptide_ids); // write ProteinIdentifications and PeptideIdentifications to IdXML From 1d98e258f6613be6942890365c46de64ca147add Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 29 Oct 2019 16:17:40 +0100 Subject: [PATCH 084/471] enable/disable SVM rescoring --- src/utils/OpenNuXL.cpp | 57 +++++++++++++++++++++++------------------- 1 file changed, 31 insertions(+), 26 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1fd3d4d3f65..2572c25720f 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -114,6 +114,7 @@ //#define FILTER_BAD_SCORES_ID_TAGS filter out some good hits //#define FILTER_AMBIGIOUS_PEAKS //#define FILTER_NO_ARBITRARY_TAG_PRESENT +#define SVM_RECALIBRATE using namespace OpenMS; using namespace OpenMS::Internal; @@ -1631,19 +1632,22 @@ static void scoreXLIons_( aa_plus_adduct_mass[m][r] = 0; } - // output ambigious masses - cout << "Ambigious residues (+adduct) masses that exactly match to other masses." << endl; - cout << "Total\tResidue\tAdduct" << endl; - for (auto& m : aa_plus_adduct_mass) + + if (debug_level_ > 0) { - double mass = m.first; - if (m.second.size() == 1) continue; // more than one residue / adduct registered for that mass - for (auto& a : m.second) + // output ambigious masses + cout << "Ambigious residues (+adduct) masses that exactly match to other masses." << endl; + cout << "Total\tResidue\tAdduct" << endl; + for (auto& m : aa_plus_adduct_mass) { - cout << mass << "\t" << a.first->getOneLetterCode() << "\t+\t" << a.second << endl; - } - } - + double mass = m.first; + if (m.second.size() == 1) continue; // more than one residue / adduct registered for that mass + for (auto& a : m.second) + { + cout << mass << "\t" << a.first->getOneLetterCode() << "\t+\t" << a.second << endl; + } + } + } map adduct_mass_count; map aa_plus_adduct_mass_count; @@ -4636,9 +4640,9 @@ static void scoreXLIons_( } } +#ifdef SVM_RECALIBRATE ///////////////////////////////////////// SVM score recalibration // find size of minority class - size_t minority_class(0); map pep_t; map pep_d; map XL_t; @@ -4650,40 +4654,41 @@ static void scoreXLIons_( const PeptideHit& ph = peptide_ids[index].getHits()[0]; bool is_target = ph.getMetaValue("target_decoy") == "target"; bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + double score = ph.getScore(); if (is_target) { if (is_XL) { - XL_t[ph.getScore()] = index; + XL_t[score] = index; } else { - pep_t[ph.getScore()] = index; + pep_t[score] = index; } } else { if (is_XL) { - XL_d[ph.getScore()] = index; + XL_d[score] = index; } else { - pep_d[ph.getScore()] = index; + pep_d[score] = index; } } } - minority_class = std::min({pep_t.size(), pep_d.size(), XL_t.size(), XL_d.size()}); + size_t minority_class = std::min({pep_t.size(), pep_d.size(), XL_t.size(), XL_d.size()}); cout << "Peptide (target/decoy)\t XL (target/decoy):" << endl; cout << pep_t.size() << "\t" << pep_d.size() << "\t" << XL_t.size() << "\t" << XL_d.size() << endl; - // keep only top elements - auto right = std::next(pep_t.begin(), (long unsigned int)(pep_t.size() - minority_class)); - pep_t.erase(pep_t.begin(), right); - pep_d.erase(pep_d.begin(), std::next(pep_d.begin(), pep_d.size() - minority_class)); + // keep only top elements (=highest scoring hits) for all classes + pep_t.erase(pep_t.begin(), next(pep_t.begin(), pep_t.size() - minority_class)); + pep_d.erase(pep_d.begin(), next(pep_d.begin(), pep_d.size() - minority_class)); XL_t.erase(XL_t.begin(), next(XL_t.begin(), XL_t.size() - minority_class)); XL_d.erase(XL_d.begin(), next(XL_d.begin(), XL_d.size() - minority_class)); + // training indices = index of peptide id that correspond to top scoring hits (of the 4 classes) set training_indices; for (auto & l : {pep_t, pep_d, XL_t, XL_d}) { @@ -4763,8 +4768,9 @@ static void scoreXLIons_( SimpleSVM svm; Param svm_param = svm.getParameters(); - svm_param.setValue("log2_C", ListUtils::create("11.0")); - svm_param.setValue("log2_gamma", ListUtils::create("-5.0")); + svm_param.setValue("kernel", "linear"); + //svm_param.setValue("log2_C", ListUtils::create("11.0")); + //svm_param.setValue("log2_gamma", ListUtils::create("-5.0")); svm.setParameters(svm_param); svm.setup(predictors, labels); vector predictions; @@ -4781,10 +4787,9 @@ static void scoreXLIons_( } peptide_ids[index].assignRanks(); } -#ifdef DEBUG_OpenNuXL - IdXMLFile().store(out_idxml + "_svm.idXML", protein_ids, peptide_ids); -#endif + // IdXMLFile().store(out_idxml + "_svm.idXML", protein_ids, peptide_ids); } +#endif fdr.apply(peptide_ids); // write ProteinIdentifications and PeptideIdentifications to IdXML From 7b68d859611784e1192ad49f38cfa250ed444658 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 30 Oct 2019 10:12:31 +0100 Subject: [PATCH 085/471] add scaling output --- src/utils/OpenNuXL.cpp | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 2572c25720f..6402281e853 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -4769,12 +4769,23 @@ static void scoreXLIons_( SimpleSVM svm; Param svm_param = svm.getParameters(); svm_param.setValue("kernel", "linear"); - //svm_param.setValue("log2_C", ListUtils::create("11.0")); - //svm_param.setValue("log2_gamma", ListUtils::create("-5.0")); svm.setParameters(svm_param); svm.setup(predictors, labels); vector predictions; svm.predict(predictions); + std::map feature_weights; + svm.getFeatureWeights(feature_weights); + cout << "Feature weights:" << endl; + for (const auto& m : feature_weights) + { + cout << m.first << "\t" << m.second << endl; + } + cout << "Feature scaling:" << endl; + auto feature_scaling = svm.getScaling(); + for (const auto& m : feature_scaling) + { + cout << m.first << "\t" << m.second.first << "\t" << m.second.second << endl; + } size_t psm_index(0); for (size_t index = 0; index != peptide_ids.size(); ++index) From a180278a70d1c7772ab4021b48530c8bd4b1cf5a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 30 Oct 2019 10:12:57 +0100 Subject: [PATCH 086/471] add getScaling to SimpleSVM --- .../include/OpenMS/ANALYSIS/SVM/SimpleSVM.h | 9 ++++++++- src/openms/source/ANALYSIS/SVM/SimpleSVM.cpp | 7 ++++++- .../class_tests/openms/source/SimpleSVM_test.cpp | 15 +++++++++++++++ 3 files changed, 29 insertions(+), 2 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/SVM/SimpleSVM.h b/src/openms/include/OpenMS/ANALYSIS/SVM/SimpleSVM.h index 6f66a7d219e..e1ce69736e7 100644 --- a/src/openms/include/OpenMS/ANALYSIS/SVM/SimpleSVM.h +++ b/src/openms/include/OpenMS/ANALYSIS/SVM/SimpleSVM.h @@ -70,6 +70,9 @@ namespace OpenMS /// Mapping from predictor name to vector of predictor values typedef std::map > PredictorMap; + /// Mapping from predictor name to predictor min and max + typedef std::map > ScaleMap; + /// SVM prediction result struct Prediction { @@ -123,6 +126,8 @@ namespace OpenMS /// Write cross-validation (parameter optimization) results to a CSV file void writeXvalResults(const String& path) const; + /// Get data range of predictors before scaling to [0, 1] + const ScaleMap& getScaling() const; protected: /// Classification performance for different param. combinations (C/gamma): typedef std::vector > SVMPerformance; @@ -148,6 +153,8 @@ namespace OpenMS /// Parameter values to try during optimization std::vector log2_C_, log2_gamma_; + ScaleMap scaling_; + /// Cross-validation results SVMPerformance performance_; @@ -155,7 +162,7 @@ namespace OpenMS static void printNull_(const char*) {} /// Scale predictor values to range 0-1 - void scaleData_(PredictorMap& predictors) const; + void scaleData_(PredictorMap& predictors); /// Convert predictors to LIBSVM format void convertData_(const PredictorMap& predictors); diff --git a/src/openms/source/ANALYSIS/SVM/SimpleSVM.cpp b/src/openms/source/ANALYSIS/SVM/SimpleSVM.cpp index 8a3d72290fc..54f9ad01920 100644 --- a/src/openms/source/ANALYSIS/SVM/SimpleSVM.cpp +++ b/src/openms/source/ANALYSIS/SVM/SimpleSVM.cpp @@ -231,7 +231,7 @@ void SimpleSVM::getFeatureWeights(map& feature_weights) const } -void SimpleSVM::scaleData_(PredictorMap& predictors) const +void SimpleSVM::scaleData_(PredictorMap& predictors) { for (PredictorMap::iterator pred_it = predictors.begin(); pred_it != predictors.end(); ++pred_it) @@ -253,9 +253,14 @@ void SimpleSVM::scaleData_(PredictorMap& predictors) const { *val_begin = (*val_begin - vmin) / range; } + scaling_[pred_it->first] = make_pair(vmin, vmax); // store old range } } +const SimpleSVM::ScaleMap& SimpleSVM::getScaling() const +{ + return scaling_; +} void SimpleSVM::convertData_(const PredictorMap& predictors) { diff --git a/src/tests/class_tests/openms/source/SimpleSVM_test.cpp b/src/tests/class_tests/openms/source/SimpleSVM_test.cpp index 258ceca3191..2ee055a691c 100644 --- a/src/tests/class_tests/openms/source/SimpleSVM_test.cpp +++ b/src/tests/class_tests/openms/source/SimpleSVM_test.cpp @@ -178,6 +178,21 @@ START_SECTION((void getFeatureWeights(map feature_weights) } END_SECTION +START_SECTION((map> void getScaling() + const)) +{ + auto scaling = svm.getScaling(feat_weights); + for (const auto& s : scaling) + { + const String name = s.first; + const pair min_max = s.second; + cout << name << "\t" << min_max.first << "\t" << min_max_second << endl; + } + TEST_EQUAL(scaling.size(), predictors.size()); // one min/max entry for every predictor +} +END_SECTION + + START_SECTION((void writeXvalResults(const String& path) const)) { string xval_file; From be230f0b95626dfbd64a0ab85c12f0c77564a572 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 12 Nov 2019 10:38:19 +0100 Subject: [PATCH 087/471] disabled nonlinear recalibration again --- .../ANALYSIS/RNPXL/RNPxlParameterParsing.cpp | 6 +- src/utils/OpenNuXL.cpp | 253 +++++++++++++++--- 2 files changed, 224 insertions(+), 35 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp index 60c22c68205..6ece8c5ac83 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp @@ -127,13 +127,13 @@ RNPxlParameterParsing::getAllFeasibleFragmentAdducts( { if (f.second.size() > 1) { - OPENMS_LOG_INFO << "Theoretical indistinguishable cross-link adducts detected: " << endl; + OPENMS_LOG_DEBUG << "Theoretical indistinguishable cross-link adducts detected: " << endl; for (auto const & m : f.second) { - OPENMS_LOG_INFO << "\tPrecursor: " << m.first << "\t and cross-linked nucleotide: " << m.second << endl; + OPENMS_LOG_DEBUG << "\tPrecursor: " << m.first << "\t and cross-linked nucleotide: " << m.second << endl; for (auto const & fragment_mass : f.first.second) { - OPENMS_LOG_INFO << "\tFragment mass: " << fragment_mass << endl; + OPENMS_LOG_DEBUG << "\tFragment mass: " << fragment_mass << endl; } } } diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 6402281e853..5b230d1c925 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -114,7 +114,7 @@ //#define FILTER_BAD_SCORES_ID_TAGS filter out some good hits //#define FILTER_AMBIGIOUS_PEAKS //#define FILTER_NO_ARBITRARY_TAG_PRESENT -#define SVM_RECALIBRATE +//#define SVM_RECALIBRATE using namespace OpenMS; using namespace OpenMS::Internal; @@ -1292,7 +1292,6 @@ score += ah.mass_error_p * 1.15386068 + isXL * 3.0 * ah.marker_ions_score + 3.0 * ah.total_MIC + ah.ladder_score; */ - return 10.0 * ah.total_loss_score + 1.0 * ah.partial_loss_score @@ -1314,9 +1313,35 @@ score += ah.mass_error_p * 1.15386068 5010 with perc auf 2- */ - - -// return -7.9010278 + 0.7545435 * ah.total_loss_score + 3.1219378 * ah.sequence_score + 0.33 * ah.mass_error_p + 0.01*ah.total_MIC; +/* + return + (ah.MIC - 0.00693372) * 0.00317232 + + (ah.Morph - 2.00693) * -5.67908 + + (ah.err - 1.8356e-05) * 0.0074405 + + (ah.immonium_score) * 3.87159 + + (isXL) * -2.8901 + + (ah.ladder_score - 0.0381864) * 2.09632 + + (ah.marker_ions_score) * 2.53656 + + (ah.mass_error_p - 0.6439) * 0.189849 + + (ah.modds - 3.37613e-07) * 9.42353 + + (ah.partial_loss_score) * 4.22367 + + (ah.pl_MIC) * 0.0770935 + + (ah.pl_Morph) * -4.25703 + + (ah.pl_err - 0.000214374) * -0.059863 + + (ah.pl_im_MIC) * -0.367491 + + (ah.pl_modds) * 2.29632 + + (ah.pl_pc_MIC) * 1.13888 + + (ah.precursor_score) * -0.597915 + + (ah.rank_product - 1) * 0.460718 + + (ah.sequence_score - 0.0218818) * -4.68762 + + (ah.tag_XLed) * 2.61103 + + (ah.tag_shifted) * -0.10144 + + (ah.tag_unshifted - 1) * 10.8324 + + (ah.total_MIC - 0.0100453) * 0.836277 + + (ah.total_loss_score - 0.106861) * 34.8899 + + (ah.wTop50 - 2) * -0.248061 + + (ah.sequence.size() - 6) * 0.00656285; // length +*/ } @@ -1742,16 +1767,19 @@ static void scoreXLIons_( spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].setName("longest_tag"); } - cout << "Distinct residue + adduct masses (including residues without shift): " << aa_plus_adduct_mass_count.size() << endl; - // Calculate background statistics on shifts - cout << "mass\tresidue\tshift:" << endl; - for (const auto& mra : aa_plus_adduct_mass) + if (debug_level_ > 0) { - double m = mra.first; - const map& residue2adduct = mra.second; - for (auto& r2a : residue2adduct) + cout << "Distinct residue + adduct masses (including residues without shift): " << aa_plus_adduct_mass_count.size() << endl; + // Calculate background statistics on shifts + cout << "mass\tresidue\tshift:" << endl; + for (const auto& mra : aa_plus_adduct_mass) { - cout << m << "\t" << r2a.first->getOneLetterCode() << "\t" << r2a.second << endl; + double m = mra.first; + const map& residue2adduct = mra.second; + for (auto& r2a : residue2adduct) + { + cout << m << "\t" << r2a.first->getOneLetterCode() << "\t" << r2a.second << endl; + } } } @@ -1774,7 +1802,7 @@ static void scoreXLIons_( } } - cout << "Total counts per residue:" << endl; + if (debug_level_ > 0) { cout << "Total counts per residue:" << endl; } #ifdef FILTER_AMBIGIOUS_PEAKS mass2high_frequency_.clear(); @@ -1787,7 +1815,10 @@ static void scoreXLIons_( double current_mass = m2c.first; size_t current_residue_count = m2c.second; size_t unmodified_residue_count = mass2count.begin()->second; - cout << aa2.first->getName() << "\t" << current_mass << "\t" << current_residue_count << endl; // aa, mass, count + if (debug_level_ > 0) + { + cout << aa2.first->getName() << "\t" << current_mass << "\t" << current_residue_count << endl; // aa, mass, count + } double frequency_normalized = (double)current_residue_count / unmodified_residue_count; // frequency relative to unmodified residue #ifdef FILTER_AMBIGIOUS_PEAKS @@ -1799,18 +1830,21 @@ static void scoreXLIons_( } } - cout << "Normalized counts per residue:" << endl; - for (const auto& aa2 : aa2mass2count) + if (debug_level_ > 0) { - auto& mass2count = aa2.second; - for (const auto m2c : mass2count) + cout << "Normalized counts per residue:" << endl; + for (const auto& aa2 : aa2mass2count) { - // normalize by counts - double current_mass = m2c.first; - size_t current_residue_count = m2c.second; - size_t unmodified_residue_count = mass2count.begin()->second; - double frequency_normalized = (double)current_residue_count / unmodified_residue_count; - cout << aa2.first->getName() << "\t" << current_mass << "\t" << frequency_normalized << endl ; // aa mass count + auto& mass2count = aa2.second; + for (const auto m2c : mass2count) + { + // normalize by counts + double current_mass = m2c.first; + size_t current_residue_count = m2c.second; + size_t unmodified_residue_count = mass2count.begin()->second; + double frequency_normalized = (double)current_residue_count / unmodified_residue_count; + cout << aa2.first->getName() << "\t" << current_mass << "\t" << frequency_normalized << endl ; // aa mass count + } } } @@ -3823,6 +3857,7 @@ static void scoreXLIons_( true); // annotate charge progresslogger.endProgress(); + progresslogger.startProgress(0, 1, "Calculate Nucleotide Tags..."); calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); // build multimap of precursor mass to scan index (and perform some mass and length based filtering) @@ -4577,7 +4612,7 @@ static void scoreXLIons_( sd += pow(m.second - mean, 2.0); } sd = sqrt(1.0/(double)i * sd); - cout << "mean ppm error: " << mean << " sd: " << sd << " 5*sd: " << 5*sd << endl; + cout << "mean ppm error: " << mean << " sd: " << sd << " 5*sd: " << 5*sd << " calculated based on " << i << " ids." << endl; if (filter_pc_mass_error) { @@ -4599,6 +4634,7 @@ static void scoreXLIons_( if (impute_decoy_medians) { + cout << "Imputing decoy medians." << endl; // calculate median score of decoys for specific meta value auto metaMedian = [](const vector & peptide_ids, const String name)->double { @@ -4699,7 +4735,8 @@ static void scoreXLIons_( { SimpleSVM::PredictorMap predictors; map labels; - + +/* StringList feature_set; feature_set << "NuXL:mass_error_p" @@ -4740,9 +4777,155 @@ static void scoreXLIons_( << "NuXL:NA_MASS_z0" << "NuXL:NA_length" << "nucleotide_mass_tags"; +*/ + + // feature set that can be calculated on-line during scoring + StringList feature_set; + feature_set + << "NuXL:mass_error_p" + << "isotope_error" + << "NuXL:err" + << "NuXL:total_loss_score" + << "NuXL:immonium_score" + << "NuXL:precursor_score" + << "NuXL:MIC" + << "NuXL:Morph" + << "NuXL:modds" + << "NuXL:partial_loss_score" + << "NuXL:pl_MIC" + << "NuXL:pl_err" + << "NuXL:pl_Morph" + << "NuXL:pl_im_MIC" + << "NuXL:pl_modds" + << "NuXL:pl_pc_MIC" + << "NuXL:total_MIC" + << "NuXL:marker_ions_score" + << "NuXL:ladder_score" + << "NuXL:sequence_score" + << "NuXL:tag_XLed" + << "NuXL:tag_unshifted" + << "NuXL:tag_shifted" + << "NuXL:rank_product" + << "NuXL:isXL" + << "NuXL:wTop50"; +/* + * +Feature weights: +NuXL:NA_MASS_z0 1.30088 +NuXL:NA_length -1.40758 +NuXL:aminoacid_id_to_max_tag_ratio 0.92732 +NuXL:aminoacid_max_tag -0.744218 +(NuXL:score 3.74526) +(score 3.74526) +NuXL:total_HS 3.90137 +NuXL:total_Morph 2.24353 + +NuXL:err 0.118611 +NuXL:immonium_score 1.70748 +NuXL:modds 1.76435 +NuXL:isXL -2.21505 +NuXL:ladder_score 2.02304 +NuXL:marker_ions_score 1.26403 +NuXL:mass_error_p 0.253748 +NuXL:partial_loss_score 0.587148 +NuXL:pl_modds 0.324605 +NuXL:pl_pc_MIC 0.176533 +NuXL:pl_im_MIC -0.2534 +NuXL:pl_MIC -0.177937 +NuXL:pl_Morph -1.58991 +NuXL:pl_err -0.0100689 +NuXL:total_loss_score 3.73413 +NuXL:MIC 0.564764 +NuXL:Morph 3.04116 +NuXL:sequence_score -1.59204 +NuXL:tag_XLed 1.63176 +NuXL:tag_shifted -0.176563 +NuXL:tag_unshifted 3.73061 +NuXL:total_MIC 0.575831 +NuXL:wTop50 -0.137687 +length 0.195985 +NuXL:precursor_score -0.513751 +NuXL:rank_product 0.349211 + + +nr_candidates 0.453777 +nucleotide_mass_tags 0.00899349 +precursor_intensity_log10 -0.383641 +variable_modifications -0.0944707 + + * */ + +/* + * mean ppm error: 0.0569701 sd: 0.447449 5*sd: 2.23725 + * Peptide (target/decoy) XL (target/decoy): + * 3975 3011 9613 4045 + * Predictor 'isotope_error' is uninformative. + * Training SVM on 12044 observations. Classes: + * - '0': 6022 observations + * - '1': 6022 observations + * Running cross-validation to find optimal SVM parameters... + * Best cross-validation performance: 83.4772% correct + * Best SVM parameters: log2_C = 5, log2_gamma = 0 + * Number of support vectors in the final model: 4252 + * Feature weights: + * NuXL:MIC 0.00317232 + * NuXL:Morph -5.67908 + * NuXL:err 0.0074405 + * NuXL:immonium_score 3.87159 + * NuXL:isXL -2.8901 + * NuXL:ladder_score 2.09632 + * NuXL:marker_ions_score 2.53656 + * NuXL:mass_error_p 0.189849 + * NuXL:modds 9.42353 + * NuXL:partial_loss_score 4.22367 + * NuXL:pl_MIC 0.0770935 + * NuXL:pl_Morph -4.25703 + * NuXL:pl_err -0.059863 + * NuXL:pl_im_MIC -0.367491 + * NuXL:pl_modds 2.29632 + * NuXL:pl_pc_MIC 1.13888 + * NuXL:precursor_score -0.597915 + * NuXL:rank_product 0.460718 + * NuXL:sequence_score -4.68762 + * NuXL:tag_XLed 2.61103 + * NuXL:tag_shifted -0.10144 + * NuXL:tag_unshifted 10.8324 + * NuXL:total_MIC 0.836277 + * NuXL:total_loss_score 34.8899 + * NuXL:wTop50 -0.248061 + * length 0.00656285 + * Feature scaling: + * NuXL:MIC 0.00693372 0.798143 + * NuXL:Morph 2.00693 50.6892 + * NuXL:err 1.8356e-05 0.0286427 + * NuXL:immonium_score 0 0.0684432 + * NuXL:isXL 0 1 + * NuXL:ladder_score 0.0381864 1.11803 + * NuXL:marker_ions_score 0 0.12167 + * NuXL:mass_error_p 0.6439 1 + * NuXL:modds 3.37613e-07 22.9923 + * NuXL:partial_loss_score 0 38.5117 + * NuXL:pl_MIC 0 0.352322 + * NuXL:pl_Morph 0 20.2243 + * NuXL:pl_err 0.000214374 0.02 + * NuXL:pl_im_MIC 0 0.115692 + * NuXL:pl_modds 0 7.26252 + * NuXL:pl_pc_MIC 0 0.33534 + * NuXL:precursor_score 0 0.299693 + * NuXL:rank_product 1 149.905 + * NuXL:sequence_score 0.0218818 1.11803 + * NuXL:tag_XLed 0 21 + * NuXL:tag_shifted 0 17 + * NuXL:tag_unshifted 1 33 + * NuXL:total_MIC 0.0100453 0.844876 + * NuXL:total_loss_score 0.106861 119.842 + * NuXL:wTop50 2 229 + * length 6 48 + */ // copy all scores in predictors ("score" + all from feature_set). // Only add labels for balanced training set + size_t current_row(0); for (size_t index = 0; index != peptide_ids.size(); ++index) { const vector& phits = peptide_ids[index].getHits(); @@ -4751,7 +4934,7 @@ static void scoreXLIons_( const PeptideHit& ph = phits[psm_rank]; bool is_target = ph.getMetaValue("target_decoy") == "target"; double score = ph.getScore(); - predictors["score"].push_back(score); + // predictors["score"].push_back(score); predictors["length"].push_back(ph.getSequence().size()); for (auto & f : feature_set) { @@ -4761,20 +4944,26 @@ static void scoreXLIons_( // only add label for training data (rank = 0 and previously selected for training) if (psm_rank == 0 && training_indices.count(index) > 0) { - labels[predictors["score"].size() - 1] = is_target; + labels[current_row] = is_target; } + ++current_row; } } SimpleSVM svm; Param svm_param = svm.getParameters(); - svm_param.setValue("kernel", "linear"); +// svm_param.setValue("kernel", "linear"); + svm_param.setValue("kernel", "RBF"); +// svm_param.setValue("log2_C", ListUtils::create("0")); +// svm_param.setValue("log2_gamma", ListUtils::create("1")); svm.setParameters(svm_param); svm.setup(predictors, labels); vector predictions; + cout << "Predicting class probabilities:" << endl; svm.predict(predictions); std::map feature_weights; svm.getFeatureWeights(feature_weights); + /* cout << "Feature weights:" << endl; for (const auto& m : feature_weights) { @@ -4786,7 +4975,7 @@ static void scoreXLIons_( { cout << m.first << "\t" << m.second.first << "\t" << m.second.second << endl; } - +*/ size_t psm_index(0); for (size_t index = 0; index != peptide_ids.size(); ++index) { @@ -4964,7 +5153,7 @@ static void scoreXLIons_( } else { - if (sufficient_PSMs_for_score_recalibration == false) OPENMS_LOG_WARN << "Too few PSMs for score recalibration. Skipped." << endl; + if (sufficient_PSMs_for_score_recalibration == false) OPENMS_LOG_WARN << "Too few PSMs for score recalibration. Skipped." << endl; } } else // no decoys From 1e834f4feac28456ccc00e4bef0d94eaea298786 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 20 Nov 2019 13:40:34 +0100 Subject: [PATCH 088/471] [FIX] ppm calculation in the presence of isotope errors --- src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp index a6c66b5e8b3..09d56385a5e 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp @@ -169,7 +169,7 @@ namespace OpenMS double peptide_weight = sequence.getMonoWeight(); String rna_name = ph.getMetaValue("NuXL:NA"); double rna_weight = ph.getMetaValue("NuXL:NA_MASS_z0"); - + int isotope_error = ph.getMetaValue("isotope_error"); // crosslink weight for different charge states double weight_z1 = (peptide_weight + rna_weight + 1.0 * Constants::PROTON_MASS_U); double weight_z2 = (peptide_weight + rna_weight + 2.0 * Constants::PROTON_MASS_U) / 2.0; @@ -178,8 +178,10 @@ namespace OpenMS double xl_weight = peptide_weight + rna_weight; double theo_mz = (xl_weight + static_cast(charge) * Constants::PROTON_MASS_U) / (double)charge; - double absolute_difference = theo_mz - mz; - double ppm_difference = Math::getPPM(mz, theo_mz); + + double corr_mz = mz - (double)isotope_error * Constants::PROTON_MASS_U / (double)charge; + double absolute_difference = theo_mz - corr_mz; + double ppm_difference = Math::getPPM(corr_mz, theo_mz); String protein_accessions; std::set accs = ph.extractProteinAccessionsSet(); From c2a72ba6befe5629666bf01366306a94e2b6db98 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 28 Nov 2019 10:52:56 +0100 Subject: [PATCH 089/471] small test file --- src/tests/class_tests/openms/source/SimpleSVM_test.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/tests/class_tests/openms/source/SimpleSVM_test.cpp b/src/tests/class_tests/openms/source/SimpleSVM_test.cpp index 2ee055a691c..cef051a0907 100644 --- a/src/tests/class_tests/openms/source/SimpleSVM_test.cpp +++ b/src/tests/class_tests/openms/source/SimpleSVM_test.cpp @@ -181,12 +181,13 @@ END_SECTION START_SECTION((map> void getScaling() const)) { - auto scaling = svm.getScaling(feat_weights); + map feat_weights; + auto scaling = svm.getScaling(); for (const auto& s : scaling) { const String name = s.first; const pair min_max = s.second; - cout << name << "\t" << min_max.first << "\t" << min_max_second << endl; + cout << name << "\t" << min_max.first << "\t" << min_max.second << endl; } TEST_EQUAL(scaling.size(), predictors.size()); // one min/max entry for every predictor } From dc6dab8f238bb7fa47154f3b801c90579e115000 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 16 Dec 2019 10:10:34 +0100 Subject: [PATCH 090/471] don't deisotope if ratio to large --- .../FILTERING/DATAREDUCTION/Deisotoper.cpp | 8 ++ src/utils/OpenNuXL.cpp | 96 +++++++++++++++---- 2 files changed, 83 insertions(+), 21 deletions(-) diff --git a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp index 6dacdbcc578..de7de14e3f7 100644 --- a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp +++ b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp @@ -162,6 +162,14 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, has_min_isopeaks = (i >= min_isopeaks); break; } + + // ratio of first isotopic peak to monoisotopic peak may not be too large + if (i == 1 && old_spectrum[p].getIntensity() / old_spectrum[extensions.back()].getIntensity() > 10.0) + { + has_min_isopeaks = (i >= min_isopeaks); + break; + } + // averagine check passed or skipped extensions.push_back(p); if (annotate_iso_peak_count) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 96900c167b5..c7d046bd462 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -116,6 +116,7 @@ //#define FILTER_AMBIGIOUS_PEAKS //#define FILTER_NO_ARBITRARY_TAG_PRESENT //#define SVM_RECALIBRATE +//#define FILTER_TOTAL_HYPERSCORE 1 using namespace OpenMS; using namespace OpenMS::Internal; @@ -684,6 +685,9 @@ class OpenNuXL : double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); + size_t comparisons(0); + size_t matches(0); + // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); @@ -713,9 +717,11 @@ class OpenNuXL : dot_product += intensity; b_mean_err += intensity * std::abs(theo_mz - exp_mz); b_ions[i] += intensity; + ++matches; peak_matched[index] = true; } } + ++comparisons; } } } @@ -748,9 +754,11 @@ class OpenNuXL : y_mean_err += intensity * std::abs(theo_mz - exp_mz); dot_product += intensity; y_ions[N-1 - i] += intensity; + ++matches; peak_matched[index] = true; } } + ++comparisons; } } @@ -820,9 +828,11 @@ class OpenNuXL : { const double intensity = exp_spectrum[index].getIntensity(); pc_MIC += intensity; + ++matches; peak_matched[index] = true; } } + ++comparisons; } } pc_MIC /= TIC; @@ -840,9 +850,11 @@ class OpenNuXL : if (!peak_matched[index]) { score += exp_spectrum[index].getIntensity(); + ++matches; peak_matched[index] = true; } } + ++comparisons; }; // see DOI: 10.1021/pr3007045 A Systematic Investigation into the Nature of Tryptic HCD Spectra @@ -916,6 +928,14 @@ class OpenNuXL : exp_spectrum.size(), exp_spectrum.back().getMZ(), (int)Morph); + +/* + modds = matchOddsScore_(comparisons, + fragment_mass_tolerance_Da, + exp_spectrum.size(), + exp_spectrum.back().getMZ(), + matches); +*/ } static void scoreShiftedLadderIons_( @@ -1294,15 +1314,15 @@ score += ah.mass_error_p * 1.15386068 + 3.0 * ah.total_MIC + ah.ladder_score; */ return - 10.0 * ah.total_loss_score - + 1.0 * ah.partial_loss_score + 1.0 * ah.total_loss_score + + 0.1 * ah.partial_loss_score + 0.1 * ah.mass_error_p - - 10.0 * ah.err - - 10.0 * ah.pl_err - + 3.0 * ah.pl_MIC - + isXL * 3.0 * ah.marker_ions_score - + 3.0 * ah.total_MIC - + 1.0 * ah.ladder_score; + - 0.1 * ah.err + - 0.1 * ah.pl_err + + 0.1 * ah.pl_MIC + + isXL * 0.1 * ah.marker_ions_score + + 0.1 * ah.total_MIC + + 0.1 * ah.ladder_score; /* -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err @@ -1882,6 +1902,28 @@ static void scoreXLIons_( ThresholdMower threshold_mower_filter; threshold_mower_filter.filterPeakMap(exp); +#ifdef _OPENMP +#pragma omp parallel for +#endif + for (SignedSize exp_index = 0; exp_index < (SignedSize)exp.size(); ++exp_index) + { + MSSpectrum & spec = exp[exp_index]; + // sort by mz + spec.sortByPosition(); + + // deisotope + Deisotoper::deisotopeAndSingleCharge(spec, + 0.05, + false, + 1, 3, + false, + 2, 10, + single_charge_spectra, + annotate_charge, + false, // no iso peak count annotation + false); // no isotope model + } + SqrtMower sqrt_mower_filter; sqrt_mower_filter.filterPeakMap(exp); @@ -1910,18 +1952,6 @@ static void scoreXLIons_( // sort by mz spec.sortByPosition(); - // deisotope - Deisotoper::deisotopeAndSingleCharge(spec, - 0.05, - false, - 1, 3, - false, - 2, 10, - single_charge_spectra, - annotate_charge, - false, // no iso peak count annotation - false); // no isotope model - if (annotate_charge) { // set Unknown charge to z=1. Otherwise we get a lot of spurious matches @@ -1984,6 +2014,8 @@ static void scoreXLIons_( spec.getFloatDataArrays()[0].push_back(TIC); spec.getFloatDataArrays()[0].setName("TIC"); } + + MzMLFile().store("debug_filtering.mzML", exp); } void filterTopNAnnotations_(vector>& ahs, const Size top_hits) @@ -4388,7 +4420,6 @@ static void scoreXLIons_( ah.sequence_score = ladderScore_(range) / (double)intensity_linear.size(); } - RankScores rankscores = rankScores_(exp_spectrum, peak_matched); ah.rank_product = rankscores.rp; ah.wTop50 = rankscores.wTop50; @@ -5009,7 +5040,30 @@ variable_modifications -0.0944707 IdXMLFile().store(out_idxml, protein_ids, peptide_ids); // generate filtered results +#ifdef FILTER_TOTAL_HYPERSCORE + for (auto & pi : peptide_ids) + { + double best_HS(0); + auto & phs = pi.getHits(); + if (phs.empty()) continue; + double max_total_HS = std::max_element(phs.begin(), phs.end(), + [] (PeptideHit const& lhs, PeptideHit const& rhs) + { + return (double)lhs.getMetaValue("NuXL:total_HS") < (double)rhs.getMetaValue("NuXL:total_HS"); + })->getMetaValue("NuXL:total_HS"); + + cout << "Max total_HS: " << max_total_HS << endl; + + auto new_end = std::remove_if(phs.begin(), phs.end(), + [&max_total_HS](const PeptideHit & ph) + { + return fabs((double)ph.getMetaValue("NuXL:total_HS") - max_total_HS) > 1e-4; + }); + phs.erase(new_end, phs.end()); + } +#else IDFilter::keepNBestHits(peptide_ids, 1); +#endif IDFilter::removeUnreferencedProteins(protein_ids, peptide_ids); // split PSMs into XLs and non-XLs but keep only best one of both From a661c34effbfee17837a6b5d7a28a6442f527c8d Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 17 Dec 2019 14:38:55 +0100 Subject: [PATCH 091/471] >5600 fast scoring, good performance on manual --- src/utils/OpenNuXL.cpp | 82 +++++++++++++++++++++++++++++++++--------- 1 file changed, 66 insertions(+), 16 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index c7d046bd462..da2aa3ceecc 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -102,6 +102,9 @@ #include #include +#include +using namespace boost::accumulators; + #ifdef _OPENMP #include #define NUMBER_OF_THREADS (omp_get_num_threads()) @@ -116,7 +119,10 @@ //#define FILTER_AMBIGIOUS_PEAKS //#define FILTER_NO_ARBITRARY_TAG_PRESENT //#define SVM_RECALIBRATE -//#define FILTER_TOTAL_HYPERSCORE 1 +#define FILTER_RANKS 1 +//#define CALCULATE_NUCLEOTIDE_TAGS 1 + +typedef accumulator_set > quantile_accu_t; using namespace OpenMS; using namespace OpenMS::Internal; @@ -1678,7 +1684,6 @@ static void scoreXLIons_( aa_plus_adduct_mass[m][r] = 0; } - if (debug_level_ > 0) { // output ambigious masses @@ -1715,12 +1720,15 @@ static void scoreXLIons_( { for (Size j = i+1; j < mzs.size(); ++j) { + if (charges[i] != charges[j]) continue; + double m = mzs[j]; double dm = m - mzs[i]; - if (charges[i] != charges[j]) continue; - const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, m) : fragment_mass_tolerance; + + if (dm * charges[i] > *adduct_mass.rbegin() + tolerance) break; + auto left = adduct_mass.lower_bound((dm * charges[i]) - tolerance); if (left == adduct_mass.end()) continue; ++in_mass_range; @@ -1766,10 +1774,15 @@ static void scoreXLIons_( spec.getFloatDataArrays()[1][0] = (double)match / (double)in_mass_range; spec.getFloatDataArrays()[1].setName("nucleotide_mass_tags"); - spec.getIntegerDataArrays().resize(3); - // calculate ranks - // + } + + // calculate ranks + cout << "Calculating ranks..." << endl; + for (auto & spec : exp) + { + if (spec.getMSLevel() != 2) continue; + // initialize original index locations vector idx(spec.size()); std::iota(idx.begin(), idx.end(), 0); @@ -1778,15 +1791,28 @@ static void scoreXLIons_( sort(idx.begin(), idx.end(), [&spec](size_t i1, size_t i2) { return spec[i1].getIntensity() > spec[i2].getIntensity(); }); + spec.getIntegerDataArrays().resize(IA_RANK_INDEX + 1); spec.getIntegerDataArrays()[IA_RANK_INDEX].clear(); for (int rank : idx) { spec.getIntegerDataArrays()[IA_RANK_INDEX].push_back(rank); } spec.getIntegerDataArrays()[IA_RANK_INDEX].setName("intensity_rank"); + } + cout << " done!" << endl; - OpenNuXLTagger tagger(0.05, 3); + cout << "Calculating longest mass tags..." << endl; + OpenNuXLTagger tagger(0.05, 3); + for (auto & spec : exp) + { + if (spec.getMSLevel() != 2) continue; + spec.getIntegerDataArrays().resize(IA_DENOVO_TAG_INDEX + 1); spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].resize(1); + spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = 0; + #ifdef CALCULATE_LONGEST_TAG spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = tagger.getLongestTag(spec).size(); + #endif spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].setName("longest_tag"); } + cout << " done!" << endl; + if (debug_level_ > 0) { @@ -3917,6 +3943,8 @@ static void scoreXLIons_( vector annotated_peptides_lock(annotated_peptides.size()); for (size_t i = 0; i != annotated_peptides_lock.size(); i++) { omp_init_lock(&(annotated_peptides_lock[i])); } #endif + vector annotated_peptides_quantiles_peptides(spectra.size(), quantile_accu_t(quantile_probability = 0.95)); + vector annotated_peptides_quantiles_XLs(spectra.size(), quantile_accu_t(quantile_probability = 0.95)); // load fasta file progresslogger.startProgress(0, 1, "Load database from FASTA file..."); @@ -4211,6 +4239,7 @@ static void scoreXLIons_( omp_set_lock(&(annotated_peptides_lock[scan_index])); #endif { + annotated_peptides_quantiles_peptides[scan_index](ah.total_loss_score); annotated_peptides[scan_index].emplace_back(move(ah)); // prevent vector from growing indefinitly (memory) but don't shrink the vector every time @@ -4446,6 +4475,7 @@ static void scoreXLIons_( omp_set_lock(&(annotated_XLs_lock[scan_index])); #endif { + annotated_peptides_quantiles_XLs[scan_index](ah.total_loss_score + ah.partial_loss_score); annotated_XLs[scan_index].emplace_back(move(ah)); // prevent vector from growing indefinitly (memory) but don't shrink the vector every time @@ -4606,6 +4636,27 @@ static void scoreXLIons_( // annotate RNPxl related information to hits and create report vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); +/* + for (Size scan_index = 0; scan_index != peptide_ids.size(); ++scan_index) + { + PeptideIdentification& pi = peptide_ids[scan_index]; + cout << "score\tpeptides\tXLs\ttype" << endl; + for (auto & ph : pi.getHits()) + { + if (ph.getMetaValue("NuXL:isXL") == "1") + { + ph.setMetaValue("NuXL:total_HS", (double)ph.getMetaValue("NuXL:total_HS") / p_square_quantile(annotated_peptides_quantiles_XLs[scan_index])); + } + else + { + ph.setMetaValue("NuXL:total_HS", (double)ph.getMetaValue("NuXL:total_HS") / p_square_quantile(annotated_peptides_quantiles_peptides[scan_index])); + } + } + } +*/ + + + /* // keep 10 bins with best 100 scores using priority queues @@ -4720,6 +4771,7 @@ static void scoreXLIons_( } } + #ifdef SVM_RECALIBRATE ///////////////////////////////////////// SVM score recalibration // find size of minority class @@ -5040,24 +5092,22 @@ variable_modifications -0.0944707 IdXMLFile().store(out_idxml, protein_ids, peptide_ids); // generate filtered results -#ifdef FILTER_TOTAL_HYPERSCORE +#ifdef FILTER_RANKS for (auto & pi : peptide_ids) { double best_HS(0); auto & phs = pi.getHits(); if (phs.empty()) continue; - double max_total_HS = std::max_element(phs.begin(), phs.end(), + double max_total_Morph = std::max_element(phs.begin(), phs.end(), [] (PeptideHit const& lhs, PeptideHit const& rhs) { - return (double)lhs.getMetaValue("NuXL:total_HS") < (double)rhs.getMetaValue("NuXL:total_HS"); - })->getMetaValue("NuXL:total_HS"); - - cout << "Max total_HS: " << max_total_HS << endl; + return (double)lhs.getMetaValue("NuXL:total_Morph") < (double)rhs.getMetaValue("NuXL:total_Morph"); + })->getMetaValue("NuXL:total_Morph"); auto new_end = std::remove_if(phs.begin(), phs.end(), - [&max_total_HS](const PeptideHit & ph) + [&max_total_Morph](const PeptideHit & ph) { - return fabs((double)ph.getMetaValue("NuXL:total_HS") - max_total_HS) > 1e-4; + return fabs((double)ph.getMetaValue("NuXL:total_Morph") - max_total_Morph) > 1e-4; }); phs.erase(new_end, phs.end()); } From 9c590ad79a4aa44a07846eeb12572ff9224865bb Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 22 Jan 2020 14:08:09 +0100 Subject: [PATCH 092/471] [FEATURE] add decoy generation to SimpleSearchEngine, annotate mass errors --- .../ANALYSIS/ID/SimpleSearchEngineAlgorithm.h | 8 +- .../ID/SimpleSearchEngineAlgorithm.cpp | 100 ++++++++++++++++-- 2 files changed, 95 insertions(+), 13 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h b/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h index 24566101ad8..27a8a3546f2 100644 --- a/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h +++ b/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h @@ -86,7 +86,7 @@ class OPENMS_DLLAPI SimpleSearchEngineAlgorithm : /// @brief filter and annotate search results /// most of the parameters are used to properly add meta data to the id objects - static void postProcessHits_(const PeakMap& exp, + void postProcessHits_(const PeakMap& exp, std::vector >& annotated_hits, std::vector& protein_ids, std::vector& peptide_ids, @@ -104,7 +104,7 @@ class OPENMS_DLLAPI SimpleSearchEngineAlgorithm : const Int precursor_min_charge, const Int precursor_max_charge, const String& enzyme, - const String& database_name); + const String& database_name) const; double precursor_mass_tolerance_; String precursor_mass_tolerance_unit_; @@ -126,6 +126,10 @@ class OPENMS_DLLAPI SimpleSearchEngineAlgorithm : String enzyme_; + bool decoys_; + + StringList annotate_psm_; + Size peptide_min_size_; Size peptide_max_size_; Size peptide_missed_cleavages_; diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index 8dc6f05d7d3..252c1f34bf9 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -62,6 +62,10 @@ #include #include #include +#include +#include + +#include #include @@ -124,6 +128,13 @@ namespace OpenMS defaults_.setValue("enzyme", "Trypsin", "The enzyme used for peptide digestion."); defaults_.setValidStrings("enzyme", all_enzymes); + defaults_.setValue("decoys", "false", "Should decoys be generated?"); + defaults_.setValidStrings("decoys", {"true","false"} ); + + defaults_.setValue("annotate:PSM", StringList{}, "Annotations added to each PSM."); + defaults_.setValidStrings("annotate:PSM", StringList{"median_fragment_error_ppm","precursor_error_ppm"}); + defaults_.setSectionDescription("annotate", "Annotation Options"); + defaults_.setValue("peptide:min_size", 7, "Minimum size a peptide must have after digestion to be considered in the search."); defaults_.setValue("peptide:max_size", 40, "Maximum size a peptide must have after digestion to be considered in the search (0 = disabled)."); defaults_.setValue("peptide:missed_cleavages", 1, "Number of missed cleavages."); @@ -164,6 +175,9 @@ namespace OpenMS peptide_motif_ = param_.getValue("peptide:motif"); report_top_hits_ = param_.getValue("report:top_hits"); + + decoys_ = param_.getValue("decoys") == "true"; + annotate_psm_ = param_.getValue("annotate:PSM"); } // static @@ -213,7 +227,6 @@ namespace OpenMS } } - // static void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, std::vector >& annotated_hits, std::vector& protein_ids, @@ -232,7 +245,7 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, const Int precursor_min_charge, const Int precursor_max_charge, const String& enzyme, - const String& database_name) + const String& database_name) const { // remove all but top n scoring #pragma omp parallel for default(none) shared(annotated_hits, top_hits) @@ -245,7 +258,10 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, annotated_hits.shrink_to_fit(); } -#pragma omp parallel for default(none) shared(annotated_hits, exp, fixed_modifications, variable_modifications, peptide_ids, max_variable_mods_per_peptide) + bool annotation_precursor_error_ppm = std::find(annotate_psm_.begin(), annotate_psm_.end(), "precursor_error_ppm") != annotate_psm_.end(); + bool annotation_fragment_error_ppm = std::find(annotate_psm_.begin(), annotate_psm_.end(), "median_fragment_error_ppm") != annotate_psm_.end(); + +#pragma omp parallel for default(none) shared(annotated_hits, exp, fixed_modifications, variable_modifications, peptide_ids, max_variable_mods_per_peptide, annotation_precursor_error_ppm, annotation_fragment_error_ppm) for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) { if (!annotated_hits[scan_index].empty()) @@ -255,19 +271,21 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, pi.setMetaValue("scan_index", static_cast(scan_index)); pi.setScoreType("hyperscore"); pi.setHigherScoreBetter(true); - pi.setRT(exp[scan_index].getRT()); - pi.setMZ(exp[scan_index].getPrecursors()[0].getMZ()); - Size charge = exp[scan_index].getPrecursors()[0].getCharge(); + const MSSpectrum& spec = exp[scan_index]; + double mz = spec.getPrecursors()[0].getMZ(); + pi.setRT(spec.getRT()); + pi.setMZ(mz); + Size charge = spec.getPrecursors()[0].getCharge(); // create full peptide hit structure from annotated hits vector phs; - for (vector::const_iterator a_it = annotated_hits[scan_index].begin(); a_it != annotated_hits[scan_index].end(); ++a_it) + for (const auto& ah : annotated_hits[scan_index]) { PeptideHit ph; ph.setCharge(charge); // get unmodified string - AASequence aas = AASequence::fromString(a_it->sequence.getString()); + AASequence aas = AASequence::fromString(ah.sequence.getString()); // reapply modifications (because for memory reasons we only stored the index and recreation is fast) vector all_modified_peptides; @@ -275,9 +293,37 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, ModifiedPeptideGenerator::applyVariableModifications(variable_modifications, aas, max_variable_mods_per_peptide, all_modified_peptides); // reannotate much more memory heavy AASequence object - AASequence fixed_and_variable_modified_peptide = all_modified_peptides[a_it->peptide_mod_index]; - ph.setScore(a_it->score); + AASequence fixed_and_variable_modified_peptide = all_modified_peptides[ah.peptide_mod_index]; + ph.setScore(ah.score); ph.setSequence(fixed_and_variable_modified_peptide); + + if (annotation_fragment_error_ppm) + { + TheoreticalSpectrumGenerator tsg; + vector > alignment; + MSSpectrum theoretical_spec; + tsg.getSpectrum(theoretical_spec, aas, 1, std::min((int)charge - 1, 2)); + SpectrumAlignment sa; + sa.getSpectrumAlignment(alignment, theoretical_spec, spec); + + vector err; + for (const auto& match : alignment) + { + double fragment_error = fabs(Math::getPPM(spec[match.second].getMZ(), theoretical_spec[match.first].getMZ())); + err.push_back(fragment_error); + } + double median_ppm_error(0); + if (!err.empty()) { median_ppm_error = Math::median(err.begin(), err.end(), false); } + ph.setMetaValue("median_fragment_error_ppm", median_ppm_error); + } + + if (annotation_precursor_error_ppm) + { + double theo_mz = aas.getMonoWeight(Residue::Full, charge)/static_cast(charge); + double ppm_difference = Math::getPPM(mz, theo_mz); + ph.setMetaValue("precursor_error_ppm", ppm_difference); + } + // store PSM phs.push_back(ph); } pi.setHits(phs); @@ -412,8 +458,40 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, ProteaseDigestion digestor; digestor.setEnzyme(enzyme_); - digestor.setMissedCleavages(peptide_missed_cleavages_); + // generate decoy protein sequences by reversing them + if (decoys_) + { + digestor.setMissedCleavages(0); + startProgress(0, 1, "Generate decoys..."); + + // append decoy proteins + const size_t old_size = fasta_db.size(); + for (size_t i = 0; i != old_size; ++i) + { + FASTAFile::FASTAEntry e = fasta_db[i]; + + std::vector output; + digestor.digest(AASequence::fromString(e.sequence), output); + // pseudo reverse protein digest + e.sequence = ""; + for (const auto & aas : output) + { + std::string s = aas.toUnmodifiedString(); + auto last = --s.end(); + std::reverse(s.begin(), last); + e.sequence += s; + } + + e.identifier = "DECOY_" + e.identifier; + fasta_db.push_back(e); + } + // randomize order of targets and decoys to introduce no global bias in the case that + // many targets have the same score as their decoy. (As we always take the first best scoring one) + std::random_shuffle(fasta_db.begin(), fasta_db.end()); + endProgress(); + digestor.setMissedCleavages(peptide_missed_cleavages_); + } startProgress(0, fasta_db.size(), "Scoring peptide models against spectra..."); // lookup for processed peptides. must be defined outside of omp section and synchronized From da2860818c18f57365a3b7d4c7c11092d0bcb7e2 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 23 Jan 2020 09:31:52 +0100 Subject: [PATCH 093/471] before refactoring --- .../ID/SimpleSearchEngineAlgorithm.cpp | 4 +- src/utils/OpenNuXL.cpp | 178 ++++++++++++++++-- 2 files changed, 163 insertions(+), 19 deletions(-) diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index 252c1f34bf9..c6e9b94b405 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -302,7 +302,7 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, TheoreticalSpectrumGenerator tsg; vector > alignment; MSSpectrum theoretical_spec; - tsg.getSpectrum(theoretical_spec, aas, 1, std::min((int)charge - 1, 2)); + tsg.getSpectrum(theoretical_spec, fixed_and_variable_modified_peptide, 1, std::min((int)charge - 1, 2)); SpectrumAlignment sa; sa.getSpectrumAlignment(alignment, theoretical_spec, spec); @@ -319,7 +319,7 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, if (annotation_precursor_error_ppm) { - double theo_mz = aas.getMonoWeight(Residue::Full, charge)/static_cast(charge); + double theo_mz = fixed_and_variable_modified_peptide.getMonoWeight(Residue::Full, charge)/static_cast(charge); double ppm_difference = Math::getPPM(mz, theo_mz); ph.setMetaValue("precursor_error_ppm", ppm_difference); } diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index da2aa3ceecc..646d6355135 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -69,6 +69,8 @@ #include // preprocessing and filtering +#include + #include #include #include @@ -102,6 +104,8 @@ #include #include +#include + #include using namespace boost::accumulators; @@ -119,7 +123,7 @@ using namespace boost::accumulators; //#define FILTER_AMBIGIOUS_PEAKS //#define FILTER_NO_ARBITRARY_TAG_PRESENT //#define SVM_RECALIBRATE -#define FILTER_RANKS 1 +//#define FILTER_RANKS 1 //#define CALCULATE_NUCLEOTIDE_TAGS 1 typedef accumulator_set > quantile_accu_t; @@ -1928,6 +1932,7 @@ static void scoreXLIons_( ThresholdMower threshold_mower_filter; threshold_mower_filter.filterPeakMap(exp); + BinnedSpectrum peak_density(MSSpectrum(), 0.05, false, 0, 0); #ifdef _OPENMP #pragma omp parallel for #endif @@ -1948,8 +1953,22 @@ static void scoreXLIons_( annotate_charge, false, // no iso peak count annotation false); // no isotope model + BinnedSpectrum bs(spec, 0.05, false, 0, 0); + bs.getBins().coeffs().cwiseMax(1); +#pragma omp critical (peak_density_access) +{ + peak_density.getBins() += bs.getBins(); +} } + ofstream dist_file; + dist_file.open(getStringOption_("in") + ".csv"); + for (double mz = 0; mz < 2500.0; mz+=0.05) + { + dist_file << peak_density.getBinIntensity(mz) << "\n"; + } + dist_file.close(); + SqrtMower sqrt_mower_filter; sqrt_mower_filter.filterPeakMap(exp); @@ -3764,16 +3783,81 @@ static void scoreXLIons_( } String in_db = getStringOption_("database"); - String out_idxml = getStringOption_("out"); - String out_tsv = getStringOption_("out_tsv"); - fast_scoring_ = getStringOption_("RNPxl:scoring") == "fast" ? true : false; - - bool generate_decoys = getFlag_("RNPxl:decoys"); Int min_precursor_charge = getIntOption_("precursor:min_charge"); Int max_precursor_charge = getIntOption_("precursor:max_charge"); double precursor_mass_tolerance = getDoubleOption_("precursor:mass_tolerance"); + double fragment_mass_tolerance = getDoubleOption_("fragment:mass_tolerance"); + bool generate_decoys = getFlag_("RNPxl:decoys"); + + // autotune (only works if non-XL peptides present) + { + SimpleSearchEngineAlgorithm sse; + vector prot_ids; + vector pep_ids; + Param p = sse.getParameters(); + p.setValue("precursor:mass_tolerance", precursor_mass_tolerance); + p.setValue("precursor:mass_tolerance_unit", getStringOption_("precursor:mass_tolerance_unit")); + p.setValue("fragment:mass_tolerance", fragment_mass_tolerance); + p.setValue("fragment:mass_tolerance_unit", getStringOption_("fragment:mass_tolerance_unit")); + p.setValue("modifications:fixed", getStringList_("modifications:fixed")); + p.setValue("modifications:variable", getStringList_("modifications:variable")); + p.setValue("modifications:variable_max_per_peptide", getIntOption_("modifications:variable_max_per_peptide")); + p.setValue("precursor:isotopes", IntList{0}); + p.setValue("decoys", generate_decoys ? "true" : "false"); + p.setValue("enzyme", getStringOption_("peptide:enzyme")); + p.setValue("annotate:PSM", StringList{"median_fragment_error_ppm", "precursor_error_ppm"}); + sse.setParameters(p); + cout << "Running autotune..." << endl; + sse.search(in_mzml, in_db, prot_ids, pep_ids); + + cout << "Calculating FDR..." << endl; + FalseDiscoveryRate fdr; + fdr.apply(pep_ids); + cout << "Filtering ..." << endl; + IDFilter::filterHitsByScore(pep_ids, 0.01); // 1% PSM-FDR + IDFilter::removeEmptyIdentifications(pep_ids); + cout << "Peptide identifications left: " << pep_ids.size() << endl; + if (pep_ids.size() > 100) + { + vector median_fragment_error_ppm; + vector precursor_error_ppm; + for (const auto& pi : pep_ids) + { + const PeptideHit& ph = pi.getHits()[0]; + if (ph.metaValueExists("median_fragment_error_ppm")) + { + //cout << ph.getMetaValue("median_fragment_error_ppm") << endl; + median_fragment_error_ppm.push_back(fabs((double)ph.getMetaValue("median_fragment_error_ppm"))); + } + if (ph.metaValueExists("precursor_error_ppm")) + { + precursor_error_ppm.push_back(fabs((double)ph.getMetaValue("precursor_error_ppm"))); + } + } + sort(median_fragment_error_ppm.begin(), median_fragment_error_ppm.end()); + sort(precursor_error_ppm.begin(), precursor_error_ppm.end()); + + // use 68-percentile as in identipy + double new_fragment_mass_tolerance = 4.0 * median_fragment_error_ppm[median_fragment_error_ppm.size() * 0.68]; + fragment_mass_tolerance = new_fragment_mass_tolerance; // set new fragment mass tolerance + double new_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.995]; + cout << "New fragment mass tolerance (ppm): " << new_fragment_mass_tolerance << endl; + cout << "Estimated max precursor mass tolerance (ppm): " << new_precursor_mass_tolerance << endl; + } + else + { + OPENMS_LOG_INFO << "autotune: too few non-cross-linked peptides found. Will keep parameters as-is." << endl; + } + } + + + String out_idxml = getStringOption_("out"); + String out_tsv = getStringOption_("out_tsv"); + + fast_scoring_ = getStringOption_("RNPxl:scoring") == "fast" ? true : false; + // true positives: assumed gaussian distribution of mass error // with sigma^2 = precursor_mass_tolerance @@ -3782,7 +3866,6 @@ static void scoreXLIons_( bool precursor_mass_tolerance_unit_ppm = (getStringOption_("precursor:mass_tolerance_unit") == "ppm"); IntList precursor_isotopes = getIntList_("precursor:isotopes"); - double fragment_mass_tolerance = getDoubleOption_("fragment:mass_tolerance"); bool fragment_mass_tolerance_unit_ppm = (getStringOption_("fragment:mass_tolerance_unit") == "ppm"); double marker_ions_tolerance = getDoubleOption_("RNPxl:marker_ions_tolerance"); @@ -4685,8 +4768,8 @@ static void scoreXLIons_( } // calculate mean ppm error from top scoring PSMs (max. 1000 considered) - double mean(0); - size_t c(0); + double mean(0), mean_negative(0), mean_positive(0); + size_t c(0), c_negative(0), c_positive(0); for (auto it = map_score2ppm.begin(); it != map_score2ppm.end(); ++it) { mean += it->second; @@ -4695,18 +4778,48 @@ static void scoreXLIons_( } if (c != 0) { mean /= c; } - double sd(0); + for (auto it = map_score2ppm.begin(); it != map_score2ppm.end(); ++it) + { + if (it->second > 0) continue; // skip positive ppm + mean_negative += it->second; + ++c_negative; + if (c_negative > 1000) break; + } + if (c_negative != 0) { mean_negative /= c_negative; } + + for (auto it = map_score2ppm.begin(); it != map_score2ppm.end(); ++it) + { + if (it->second < 0) continue; // skip negative ppm + mean_positive += it->second; + ++c_positive; + if (c_positive > 1000) break; + } + if (c_positive != 0) { mean_positive /= c_positive; } + + double sd(0), sd_negative(0), sd_positive(0); auto it = map_score2ppm.begin(); for (size_t i = 0; i != c; ++i) { sd += pow(it->second - mean, 2.0); + if (it->second < 0) sd_negative += pow(it->second - mean, 2.0); + if (it->second > 0) sd_positive += pow(it->second - mean, 2.0); ++it; } if (c != 0) { sd = sqrt(1.0/static_cast(c) * sd); + if (c_negative != 0) + { + sd_negative = sqrt(1.0/static_cast(c_negative) * sd_negative); + } + if (c_positive != 0) + { + sd_positive = sqrt(1.0/static_cast(c_positive) * sd_positive); + } cout << "mean ppm error: " << mean << " sd: " << sd << " 5*sd: " << 5*sd << " calculated based on " << c << " best ids." << endl; + cout << "mean negative ppm error: " << mean_negative << " sd: " << sd_negative << " 5*sd: " << 5*sd_negative << " calculated based on " << c_negative << " best ids." << endl; + cout << "mean positive ppm error: " << mean_positive << " sd: " << sd_positive << " 5*sd: " << 5*sd_positive << " calculated based on " << c_positive << " best ids." << endl; } if (filter_pc_mass_error && c != 0) @@ -4747,13 +4860,33 @@ static void scoreXLIons_( std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); return Math::median(decoy_XL_scores.begin(), decoy_XL_scores.end()); }; - + + // all medians + auto metaMean = [](const vector & peptide_ids, const String name)->double + { + vector decoy_XL_scores; + for (const auto & pi : peptide_ids) + { + for (const auto & ph : pi.getHits()) + { + const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); + if (!is_XL) continue; + double score = ph.getMetaValue(name); + decoy_XL_scores.push_back(score); + } + } + std::sort(decoy_XL_scores.begin(), decoy_XL_scores.end(), greater()); + return Math::mean(decoy_XL_scores.begin(), decoy_XL_scores.end()); + }; + map medians; for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) { - medians[mn] = metaMedian(peptide_ids, mn); +// medians[mn] = metaMedian(peptide_ids, mn); + medians[mn] = metaMean(peptide_ids, mn); } + size_t imputed(0); for (auto & pi : peptide_ids) { for (auto & ph : pi.getHits()) @@ -4765,10 +4898,12 @@ static void scoreXLIons_( { ph.setMetaValue(mn, medians[mn]); // impute missing with medians } + ++imputed; } } pi.assignRanks(); } + cout << "Imputed XL features in " << imputed << " linear peptides." << endl; } @@ -4783,7 +4918,7 @@ static void scoreXLIons_( for (size_t index = 0; index != peptide_ids.size(); ++index) { if (peptide_ids[index].getHits().empty()) continue; - const PeptideHit& ph = peptide_ids[index].getHits()[0]; + const PeptideHit& ph = peptide_ids[index].getHits()[0]; // get best match to current spectrum bool is_target = ph.getMetaValue("target_decoy") == "target"; bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); double score = ph.getScore(); @@ -4814,6 +4949,8 @@ static void scoreXLIons_( cout << "Peptide (target/decoy)\t XL (target/decoy):" << endl; cout << pep_t.size() << "\t" << pep_d.size() << "\t" << XL_t.size() << "\t" << XL_d.size() << endl; + if (minority_class > 250) minority_class = 250; + // keep only top elements (=highest scoring hits) for all classes pep_t.erase(pep_t.begin(), next(pep_t.begin(), pep_t.size() - minority_class)); pep_d.erase(pep_d.begin(), next(pep_d.begin(), pep_d.size() - minority_class)); @@ -4904,6 +5041,8 @@ static void scoreXLIons_( << "NuXL:rank_product" << "NuXL:isXL" << "NuXL:wTop50"; + + /* * Feature weights: @@ -5048,8 +5187,8 @@ variable_modifications -0.0944707 SimpleSVM svm; Param svm_param = svm.getParameters(); -// svm_param.setValue("kernel", "linear"); - svm_param.setValue("kernel", "RBF"); + svm_param.setValue("kernel", "linear"); +// svm_param.setValue("kernel", "RBF"); // svm_param.setValue("log2_C", ListUtils::create("0")); // svm_param.setValue("log2_gamma", ListUtils::create("1")); svm.setParameters(svm_param); @@ -5095,9 +5234,10 @@ variable_modifications -0.0944707 #ifdef FILTER_RANKS for (auto & pi : peptide_ids) { - double best_HS(0); auto & phs = pi.getHits(); if (phs.empty()) continue; + if (static_cast(phs[0].getMetaValue("NuXL:isXL")) == 0) continue; // only rerank cross-links + double max_total_Morph = std::max_element(phs.begin(), phs.end(), [] (PeptideHit const& lhs, PeptideHit const& rhs) { @@ -5174,13 +5314,17 @@ variable_modifications -0.0944707 // run percolator on idXML String perc_out = out_idxml; perc_out.substitute(".idXML", "_perc.idXML"); + String weights_out = out_idxml; + weights_out.substitute(".idXML", ".weights"); + QStringList process_params; process_params << "-in" << out_idxml.toQString() << "-out" << perc_out.toQString() << "-percolator_executable" << percolator_executable.toQString() << "-train-best-positive" << "-score_type" << "svm" - << "-post-processing-tdc"; + << "-post-processing-tdc" + << "-weights" << weights_out.toQString(); #if DEBUG_OpenNuXL process_params << "-out_pout_target" << "merged_target.tab" << "-out_pout_decoy" << "merged_decoy.tab"; #endif From 91acc55a1668ec5404c9d6b151781147c65803bd Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 23 Jan 2020 09:32:39 +0100 Subject: [PATCH 094/471] [FEATURE] add static training option to percolator --- src/topp/PercolatorAdapter.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/topp/PercolatorAdapter.cpp b/src/topp/PercolatorAdapter.cpp index 42d8b32a310..3e950295755 100644 --- a/src/topp/PercolatorAdapter.cpp +++ b/src/topp/PercolatorAdapter.cpp @@ -274,6 +274,7 @@ class PercolatorAdapter : registerFlag_("quick-validation", "Quicker execution by reduced internal cross-validation.", is_advanced_option); registerOutputFile_("weights", "", "", "Output final weights to the given file", !is_required, is_advanced_option); registerInputFile_("init-weights", "", "", "Read initial weights to the given file", !is_required, is_advanced_option); + registerFlag_("static", "Use static model (requires init-weights parameter to be set)", is_advanced_option); registerStringOption_("default-direction", "", "", "The most informative feature given as the feature name, can be negated to indicate that a lower value is better.", !is_required, is_advanced_option); registerIntOption_("verbose", "", 2, "Set verbosity of output: 0=no processing info, 5=all.", !is_required, is_advanced_option); registerFlag_("unitnorm", "Use unit normalization [0-1] instead of standard deviation normalization", is_advanced_option); @@ -1020,6 +1021,7 @@ class PercolatorAdapter : if (getFlag_("quick-validation")) arguments << "-x"; if (getFlag_("post-processing-tdc")) arguments << "-Y"; if (getFlag_("train-best-positive")) arguments << "--train-best-positive"; + if (getFlag_("static")) arguments << "--static"; String weights_file = getStringOption_("weights"); String init_weights_file = getStringOption_("init-weights"); @@ -1251,6 +1253,7 @@ class PercolatorAdapter : search_parameters.setMetaValue("Percolator:maxiter", getIntOption_("maxiter")); search_parameters.setMetaValue("Percolator:subset-max-train", getIntOption_("subset-max-train")); search_parameters.setMetaValue("Percolator:quick-validation", getFlag_("quick-validation")); + search_parameters.setMetaValue("Percolator:static", getFlag_("static")); search_parameters.setMetaValue("Percolator:weights", getStringOption_("weights")); search_parameters.setMetaValue("Percolator:init-weights", getStringOption_("init-weights")); search_parameters.setMetaValue("Percolator:default-direction", getStringOption_("default-direction")); From 63766097f6c328b3498b58a60f64142b7fdd65aa Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 30 Jan 2020 15:50:33 +0100 Subject: [PATCH 095/471] [FEATURE] add nested cross-validation parameter --- src/topp/PercolatorAdapter.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/topp/PercolatorAdapter.cpp b/src/topp/PercolatorAdapter.cpp index 3e950295755..b13be63de0b 100644 --- a/src/topp/PercolatorAdapter.cpp +++ b/src/topp/PercolatorAdapter.cpp @@ -271,6 +271,7 @@ class PercolatorAdapter : registerDoubleOption_("testFDR", "", 0.01, "False discovery rate threshold for evaluating best cross validation result and the reported end result.", !is_required, is_advanced_option); registerDoubleOption_("trainFDR", "", 0.01, "False discovery rate threshold to define positive examples in training. Set to testFDR if 0.", !is_required, is_advanced_option); registerIntOption_("maxiter", "", 10, "Maximal number of iterations", !is_required, is_advanced_option); + registerIntOption_("nested-xval-bins", "", 1, "Number of nested cross-validation bins in the 3 splits.", !is_required, is_advanced_option); registerFlag_("quick-validation", "Quicker execution by reduced internal cross-validation.", is_advanced_option); registerOutputFile_("weights", "", "", "Output final weights to the given file", !is_required, is_advanced_option); registerInputFile_("init-weights", "", "", "Read initial weights to the given file", !is_required, is_advanced_option); @@ -1022,7 +1023,9 @@ class PercolatorAdapter : if (getFlag_("post-processing-tdc")) arguments << "-Y"; if (getFlag_("train-best-positive")) arguments << "--train-best-positive"; if (getFlag_("static")) arguments << "--static"; - + Int nested_xval_bins = getIntOption_("nested-xval-bins"); + if (nested_xval_bins > 1) arguments << "--nested-xval-bins" << String(nested_xval_bins).toQString(); + String weights_file = getStringOption_("weights"); String init_weights_file = getStringOption_("init-weights"); String default_search_direction = getStringOption_("default-direction"); From f406923e7916d52bf05e0f6af75ce23dabb9521a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 30 Jan 2020 15:51:14 +0100 Subject: [PATCH 096/471] [FEATURE] autotune feature --- src/utils/OpenNuXL.cpp | 81 +++++++++++++++++++++++++++--------------- 1 file changed, 52 insertions(+), 29 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 646d6355135..019bfe60da7 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -554,7 +554,7 @@ class OpenNuXL : registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); registerStringList_("filter", "", {"filter_pc_mass_error", "impute_decoy_medians"}, "Filtering steps applied to results.", false, true); - setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores"}); + setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune"}); } @@ -566,6 +566,7 @@ class OpenNuXL : || tlss_total_MIC < 0.01); } + static bool badPartialLossScore(float tlss_Morph, float plss_Morph, float plss_MIC, float plss_im_MIC, float plss_pc_MIC, float marker_ions_score) { if (plss_Morph + tlss_Morph < 5.03) return true; // less than 5 peaks? 3% TIC @@ -576,6 +577,21 @@ class OpenNuXL : return (plss_Morph < MIN_SHIFTED_IONS && plss_im_MIC < 0.03); } + +/* + // less strict filtering + static bool badPartialLossScore(float tlss_Morph, float plss_Morph, float plss_MIC, float plss_im_MIC, float plss_pc_MIC, float marker_ions_score) + { + if (plss_Morph + tlss_Morph < 3.0) return true; // less than 3 matched peaks? + + // no signal in NA specific peaks? + if (plss_MIC + plss_im_MIC + plss_pc_MIC + marker_ions_score == 0.0) return true; + + // if we don't see shifted ladder ions, we need at least some signal in the shifted immonium ions + return false; + } +*/ + /* @param N number of theoretical peaks @param peak_in_spectrum number of experimental peaks @@ -1050,7 +1066,7 @@ class OpenNuXL : { for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { - for (Size i = 0; i < partial_loss_template_z1_y_ions.size(); ++i) + for (Size i = 1; i < partial_loss_template_z1_y_ions.size(); ++i) // Note that we start at (i=1 -> y2) as trypsin would otherwise not cut { const double theo_mz = (partial_loss_template_z1_y_ions[i] + fa.mass + (z-1) * Constants::PROTON_MASS_U) / z; @@ -1669,7 +1685,7 @@ static void scoreXLIons_( } } - // mass shift to residue + adduct (including no adduct) + // mass shift to residue + adduct (including no adduct, see below) map > aa_plus_adduct_mass; auto residues = ResidueDB::getInstance()->getResidues("Natural19WithoutI"); @@ -1691,17 +1707,21 @@ static void scoreXLIons_( if (debug_level_ > 0) { // output ambigious masses - cout << "Ambigious residues (+adduct) masses that exactly match to other masses." << endl; - cout << "Total\tResidue\tAdduct" << endl; + ofstream of; + of.open(getStringOption_("in") + ".ambigious_masses.csv"); + of << "Ambigious residues (+adduct) masses that exactly match to other masses." << endl; + of << "Total\tResidue\tAdduct" << endl; for (auto& m : aa_plus_adduct_mass) { double mass = m.first; - if (m.second.size() == 1) continue; // more than one residue / adduct registered for that mass + if (m.second.size() == 1) continue; + // more than one residue / adduct registered for that mass for (auto& a : m.second) { - cout << mass << "\t" << a.first->getOneLetterCode() << "\t+\t" << a.second << endl; + of << mass << "\t" << a.first->getOneLetterCode() << "\t" << a.second << "\n"; } - } + } + of.close(); } map adduct_mass_count; @@ -1932,7 +1952,6 @@ static void scoreXLIons_( ThresholdMower threshold_mower_filter; threshold_mower_filter.filterPeakMap(exp); - BinnedSpectrum peak_density(MSSpectrum(), 0.05, false, 0, 0); #ifdef _OPENMP #pragma omp parallel for #endif @@ -1953,21 +1972,8 @@ static void scoreXLIons_( annotate_charge, false, // no iso peak count annotation false); // no isotope model - BinnedSpectrum bs(spec, 0.05, false, 0, 0); - bs.getBins().coeffs().cwiseMax(1); -#pragma omp critical (peak_density_access) -{ - peak_density.getBins() += bs.getBins(); -} } - ofstream dist_file; - dist_file.open(getStringOption_("in") + ".csv"); - for (double mz = 0; mz < 2500.0; mz+=0.05) - { - dist_file << peak_density.getBinIntensity(mz) << "\n"; - } - dist_file.close(); SqrtMower sqrt_mower_filter; sqrt_mower_filter.filterPeakMap(exp); @@ -1988,9 +1994,9 @@ static void scoreXLIons_( NLargest nlargest_filter = NLargest(400); -#ifdef _OPENMP + BinnedSpectrum peak_density(MSSpectrum(), 0.05, false, 0, 0); + #pragma omp parallel for -#endif for (SignedSize exp_index = 0; exp_index < (SignedSize)exp.size(); ++exp_index) { MSSpectrum & spec = exp[exp_index]; @@ -2051,6 +2057,12 @@ static void scoreXLIons_( cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << "\t" << ia[i] << endl; #endif + BinnedSpectrum bs(spec, 0.05, false, 0, 0); + bs.getBins().coeffs().cwiseMax(1); + +#pragma omp critical (peak_density_access) + peak_density.getBins() += bs.getBins(); + // calculate TIC and store in float data array double TIC = std::accumulate(spec.begin(), spec.end(), 0.0, [&](double a, const Peak1D& b) { return a + b.getIntensity(); }); @@ -2060,6 +2072,14 @@ static void scoreXLIons_( spec.getFloatDataArrays()[0].setName("TIC"); } + ofstream dist_file; + dist_file.open(getStringOption_("in") + ".fragment_dist.csv"); + dist_file << "m/z\tfragments" << "\n"; + for (double mz = 0; mz < 2500.0; mz+=0.05) + { + dist_file << mz << "\t" << peak_density.getBinIntensity(mz) << "\n"; + } + dist_file.close(); MzMLFile().store("debug_filtering.mzML", exp); } @@ -3791,7 +3811,13 @@ static void scoreXLIons_( double fragment_mass_tolerance = getDoubleOption_("fragment:mass_tolerance"); bool generate_decoys = getFlag_("RNPxl:decoys"); + StringList filter = getStringList_("filter"); + bool filter_pc_mass_error = find(filter.begin(), filter.end(), "filter_pc_mass_error") != filter.end(); + bool impute_decoy_medians = find(filter.begin(), filter.end(), "impute_decoy_medians") != filter.end(); + bool filter_bad_partial_loss_scores = find(filter.begin(), filter.end(), "filter_bad_partial_loss_scores") != filter.end(); + bool autotune = find(filter.begin(), filter.end(), "autotune") != filter.end(); // autotune (only works if non-XL peptides present) + if (autotune) { SimpleSearchEngineAlgorithm sse; vector prot_ids; @@ -3920,11 +3946,6 @@ static void scoreXLIons_( bool cysteine_adduct = getFlag_("RNPxl:CysteineAdduct"); - StringList filter = getStringList_("filter"); - bool filter_pc_mass_error = find(filter.begin(), filter.end(), "filter_pc_mass_error") != filter.end(); - bool impute_decoy_medians = find(filter.begin(), filter.end(), "impute_decoy_medians") != filter.end(); - bool filter_bad_partial_loss_scores = find(filter.begin(), filter.end(), "filter_bad_partial_loss_scores") != filter.end(); - // generate mapping from empirical formula to mass and empirical formula to (one or more) precursor adducts RNPxlModificationMassesResult mm; if (max_nucleotide_length != 0) @@ -5324,6 +5345,8 @@ variable_modifications -0.0944707 << "-train-best-positive" << "-score_type" << "svm" << "-post-processing-tdc" +// << "-nested-xval-bins" << "3" + //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice << "-weights" << weights_out.toQString(); #if DEBUG_OpenNuXL process_params << "-out_pout_target" << "merged_target.tab" << "-out_pout_decoy" << "merged_decoy.tab"; From 5a1767115bcd46048571cbd88d1828b45a0a8ab0 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 30 Jan 2020 16:45:31 +0100 Subject: [PATCH 097/471] good result on in vivo with autotune and slow scoring --- src/utils/OpenNuXL.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 019bfe60da7..b3f1b136e2e 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -3816,6 +3816,7 @@ static void scoreXLIons_( bool impute_decoy_medians = find(filter.begin(), filter.end(), "impute_decoy_medians") != filter.end(); bool filter_bad_partial_loss_scores = find(filter.begin(), filter.end(), "filter_bad_partial_loss_scores") != filter.end(); bool autotune = find(filter.begin(), filter.end(), "autotune") != filter.end(); + // autotune (only works if non-XL peptides present) if (autotune) { From 2c9d4f65f5b7c035ec24484860a990df0eb86fa9 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 5 Feb 2020 16:25:38 +0100 Subject: [PATCH 098/471] 5635 on alex data --- src/utils/OpenNuXL.cpp | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index b3f1b136e2e..1c0e90be1b0 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -553,7 +553,7 @@ class OpenNuXL : registerDoubleOption_("RNPxl:filter_small_peptide_mass", "", 600.0, "Filter precursor that can only correspond to non-crosslinks by mass.", false, true); registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); - registerStringList_("filter", "", {"filter_pc_mass_error", "impute_decoy_medians"}, "Filtering steps applied to results.", false, true); + registerStringList_("filter", "", {"filter_pc_mass_error", "autotune"}, "Filtering steps applied to results.", false, true); setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune"}); } @@ -1025,6 +1025,7 @@ class OpenNuXL : for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { for (Size i = 0; i < partial_loss_template_z1_b_ions.size(); ++i) + { const double theo_mz = (partial_loss_template_z1_b_ions[i] + fa.mass + diff2b + (z-1) * Constants::PROTON_MASS_U) / z; @@ -1066,7 +1067,7 @@ class OpenNuXL : { for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { - for (Size i = 1; i < partial_loss_template_z1_y_ions.size(); ++i) // Note that we start at (i=1 -> y2) as trypsin would otherwise not cut + for (Size i = 1; i < partial_loss_template_z1_y_ions.size(); ++i) // Note that we start at (i=1 -> y2) as trypsin would otherwise not cut at cross-linking site { const double theo_mz = (partial_loss_template_z1_y_ions[i] + fa.mass + (z-1) * Constants::PROTON_MASS_U) / z; @@ -3860,18 +3861,21 @@ static void scoreXLIons_( } if (ph.metaValueExists("precursor_error_ppm")) { - precursor_error_ppm.push_back(fabs((double)ph.getMetaValue("precursor_error_ppm"))); + precursor_error_ppm.push_back((double)ph.getMetaValue("precursor_error_ppm")); } } - sort(median_fragment_error_ppm.begin(), median_fragment_error_ppm.end()); + sort(median_fragment_error_ppm.begin(), median_fragment_error_ppm.end()); sort(precursor_error_ppm.begin(), precursor_error_ppm.end()); // use 68-percentile as in identipy double new_fragment_mass_tolerance = 4.0 * median_fragment_error_ppm[median_fragment_error_ppm.size() * 0.68]; fragment_mass_tolerance = new_fragment_mass_tolerance; // set new fragment mass tolerance - double new_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.995]; + double left_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.005]; + double median_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.5]; + double right_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.995]; + cout << "New fragment mass tolerance (ppm): " << new_fragment_mass_tolerance << endl; - cout << "Estimated max precursor mass tolerance (ppm): " << new_precursor_mass_tolerance << endl; + cout << "Estimated precursor mass tolerance (ppm): " << left_precursor_mass_tolerance << "\t" << median_precursor_mass_tolerance << "\t" << right_precursor_mass_tolerance << endl; } else { @@ -5345,6 +5349,7 @@ variable_modifications -0.0944707 << "-percolator_executable" << percolator_executable.toQString() << "-train-best-positive" << "-score_type" << "svm" + << "-unitnorm" << "-post-processing-tdc" // << "-nested-xval-bins" << "3" //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice From 2d5867c5d09005db392ffb808573207cd52aa5f5 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 19 Feb 2020 09:48:52 +0100 Subject: [PATCH 099/471] id filter, multiple fdrs --- src/utils/OpenNuXL.cpp | 124 +++++++++++++++++++++++++++-------------- 1 file changed, 83 insertions(+), 41 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1c0e90be1b0..4c80964a002 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -472,8 +472,8 @@ class OpenNuXL : registerTOPPSubsection_("report", "Reporting Options"); registerIntOption_("report:top_hits", "", 1, "Maximum number of top scoring hits per spectrum that are reported.", false, true); - registerDoubleOption_("report:peptideFDR", "", 0.0, "Maximum q-value of non-cross-linked peptides. (0 = disabled)", false, true); - registerDoubleOption_("report:xlFDR", "", 0.0, "Maximum q-value of cross-linked peptides. (0 = disabled)", false, true); + registerDoubleOption_("report:peptideFDR", "", 0.0, "Maximum q-value of non-cross-linked peptides. (0 = disabled).", false, true); + registerDoubleList_("report:xlFDR", "", { 0.0 }, "Maximum q-value of cross-linked peptides. (0 = disabled). If multiple values are provided, multiple output files will be created.", false, true); registerInputFile_("percolator_executable", "", // choose the default value according to the platform where it will be executed @@ -553,8 +553,8 @@ class OpenNuXL : registerDoubleOption_("RNPxl:filter_small_peptide_mass", "", 600.0, "Filter precursor that can only correspond to non-crosslinks by mass.", false, true); registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); - registerStringList_("filter", "", {"filter_pc_mass_error", "autotune"}, "Filtering steps applied to results.", false, true); - setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune"}); + registerStringList_("filter", "", {"filter_pc_mass_error", "autotune", "idfilter"}, "Filtering steps applied to results.", false, true); + setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune", "idfilter"}); } @@ -3817,8 +3817,10 @@ static void scoreXLIons_( bool impute_decoy_medians = find(filter.begin(), filter.end(), "impute_decoy_medians") != filter.end(); bool filter_bad_partial_loss_scores = find(filter.begin(), filter.end(), "filter_bad_partial_loss_scores") != filter.end(); bool autotune = find(filter.begin(), filter.end(), "autotune") != filter.end(); + bool idfilter = find(filter.begin(), filter.end(), "idfilter") != filter.end(); // autotune (only works if non-XL peptides present) + set skip_peptide_spectrum; if (autotune) { SimpleSearchEngineAlgorithm sse; @@ -3829,10 +3831,17 @@ static void scoreXLIons_( p.setValue("precursor:mass_tolerance_unit", getStringOption_("precursor:mass_tolerance_unit")); p.setValue("fragment:mass_tolerance", fragment_mass_tolerance); p.setValue("fragment:mass_tolerance_unit", getStringOption_("fragment:mass_tolerance_unit")); - p.setValue("modifications:fixed", getStringList_("modifications:fixed")); - p.setValue("modifications:variable", getStringList_("modifications:variable")); - p.setValue("modifications:variable_max_per_peptide", getIntOption_("modifications:variable_max_per_peptide")); - p.setValue("precursor:isotopes", IntList{0}); + StringList var_mods = getStringList_("modifications:variable"); + if (find(var_mods.begin(), var_mods.end(), "Phospho (S)") != var_mods.end()) { var_mods.push_back("Phospho (S)"); } + if (find(var_mods.begin(), var_mods.end(), "Phospho (T)") != var_mods.end()) { var_mods.push_back("Phospho (T)"); } + if (find(var_mods.begin(), var_mods.end(), "Phospho (Y)") != var_mods.end()) { var_mods.push_back("Phospho (Y)"); } + if (find(var_mods.begin(), var_mods.end(), "Oxidation (M)") != var_mods.end()) { var_mods.push_back("Oxidation (M)"); } + StringList fixed_mods = getStringList_("modifications:fixed"); + p.setValue("modifications:fixed", fixed_mods); + p.setValue("modifications:variable", var_mods); + p.setValue("modifications:variable_max_per_peptide", 2); + p.setValue("peptide:missed_cleavages", 2); + p.setValue("precursor:isotopes", IntList{0, 1}); p.setValue("decoys", generate_decoys ? "true" : "false"); p.setValue("enzyme", getStringOption_("peptide:enzyme")); p.setValue("annotate:PSM", StringList{"median_fragment_error_ppm", "precursor_error_ppm"}); @@ -3847,6 +3856,16 @@ static void scoreXLIons_( IDFilter::filterHitsByScore(pep_ids, 0.01); // 1% PSM-FDR IDFilter::removeEmptyIdentifications(pep_ids); cout << "Peptide identifications left: " << pep_ids.size() << endl; + + // ID-filter part for linear peptides + if (idfilter) + { + for (const auto& pi : pep_ids) + { + skip_peptide_spectrum.insert((String)pi.getMetaValue("spectrum_reference")); // get native id + } + } + if (pep_ids.size() > 100) { vector median_fragment_error_ppm; @@ -3882,14 +3901,14 @@ static void scoreXLIons_( OPENMS_LOG_INFO << "autotune: too few non-cross-linked peptides found. Will keep parameters as-is." << endl; } } - - + + OPENMS_LOG_INFO << "IDFilter excludes " << skip_peptide_spectrum.size() << " spectra." << endl; + String out_idxml = getStringOption_("out"); String out_tsv = getStringOption_("out_tsv"); fast_scoring_ = getStringOption_("RNPxl:scoring") == "fast" ? true : false; - // true positives: assumed gaussian distribution of mass error // with sigma^2 = precursor_mass_tolerance boost::math::normal gaussian_mass_error(0.0, sqrt(precursor_mass_tolerance)); @@ -3928,7 +3947,7 @@ static void scoreXLIons_( size_t report_top_hits = (size_t)getIntOption_("report:top_hits"); double peptide_FDR = getDoubleOption_("report:peptideFDR"); - double XL_FDR = getDoubleOption_("report:xlFDR"); + DoubleList XL_FDR = getDoubleList_("report:xlFDR"); // string format: target,formula e.g. "A=C10H14N5O7P", ..., "U=C10H14N5O7P", "X=C9H13N2O8PS" where X represents tU StringList target_nucleotides = getStringList_("RNPxl:target_nucleotides"); @@ -4410,6 +4429,9 @@ static void scoreXLIons_( { const Size & scan_index = l->second.first; const PeakSpectrum & exp_spectrum = spectra[scan_index]; +/////////////////////////////////////////////////////////////////////////// basically an ID-filter reimplementation + if (skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) { continue; } +////////////////////////////////////////// #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } @@ -4476,9 +4498,6 @@ static void scoreXLIons_( plss_pc_MIC(0), plss_im_MIC(0); - std::fill(b_ions.begin(), b_ions.end(), 0); - std::fill(y_ions.begin(), y_ions.end(), 0); - scoreXLIons_(partial_loss_modification, iip, exp_spectrum, @@ -4517,7 +4536,6 @@ static void scoreXLIons_( ah.sequence = *cit; // copy StringView ah.peptide_mod_index = mod_pep_idx; - /* /////////////////////////////////////////////////////////////////////////////// test recalculate hyperscore on merged XL/non-XL ladders size_t y_ion_count = std::count_if(y_ions.begin(), y_ions.end(), [](double d) { return d > 1e-6; }); @@ -4526,7 +4544,8 @@ static void scoreXLIons_( dot_product = std::accumulate(intensity_linear.begin(), intensity_linear.end(), dot_product); const double yFact = logfactorial_(y_ion_count); const double bFact = logfactorial_(b_ion_count); - hyperScore = log1p(dot_product) + yFact + bFact; + partial_loss_sub_score = log1p(dot_product) + yFact + bFact; +////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// */ ah.total_loss_score = hyperScore; ah.MIC = tlss_MIC; @@ -4606,6 +4625,14 @@ static void scoreXLIons_( for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; + auto mod_combinations_it = mm.mod_combinations.begin(); + std::advance(mod_combinations_it, rna_mod_index); + const String& precursor_rna_adduct = *mod_combinations_it->second.begin(); + MSSpectrum& exp_spectrum = spectra[scan_index]; + + if (precursor_rna_adduct != "none" && skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) continue; + + #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } @@ -5315,24 +5342,31 @@ variable_modifications -0.0944707 { IDFilter::filterHitsByScore(pep_pi, peptide_FDR); } - - if (XL_FDR > 0.0 && XL_FDR < 1.0) - { - IDFilter::filterHitsByScore(xl_pi, XL_FDR); - } - String out2(out_idxml); - out2.substitute(".idXML", "_"); - { - vector tmp_prots = protein_ids; - IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); - IdXMLFile().store(out2 + String::number(XL_FDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); - } { + String out2(out_idxml); + out2.substitute(".idXML", "_"); vector tmp_prots = protein_ids; IDFilter::removeUnreferencedProteins(tmp_prots, pep_pi); IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", tmp_prots, pep_pi); } + std::replace(XL_FDR.begin(), XL_FDR.end(), 0.0, 1.0); + sort(XL_FDR.begin(), XL_FDR.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters + for (double xlFDR : XL_FDR) + { + if (xlFDR > 0.0 && xlFDR < 1.0) + { + IDFilter::filterHitsByScore(xl_pi, xlFDR); + } + { + String out2(out_idxml); + out2.substitute(".idXML", "_"); + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); + IdXMLFile().store(out2 + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); + } + } + String percolator_executable = getStringOption_("percolator_executable"); bool sufficient_PSMs_for_score_recalibration = (xl_pi.size() + pep_pi.size()) > 1000; if (!percolator_executable.empty() && sufficient_PSMs_for_score_recalibration) // only try to call percolator if we have some PSMs @@ -5422,23 +5456,31 @@ variable_modifications -0.0944707 { IDFilter::filterHitsByScore(pep_pi, peptide_FDR); } - - if (XL_FDR > 0.0 && XL_FDR < 1.0) - { - IDFilter::filterHitsByScore(xl_pi, XL_FDR); - } - String out2(out_idxml); - out2.substitute(".idXML", "_perc_"); - { - vector tmp_prots = protein_ids; - IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); - IdXMLFile().store(out2 + String::number(XL_FDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); - } { + String out2(out_idxml); + out2.substitute(".idXML", "_perc_"); vector tmp_prots = protein_ids; IDFilter::removeUnreferencedProteins(tmp_prots, pep_pi); IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", tmp_prots, pep_pi); } + + std::replace(XL_FDR.begin(), XL_FDR.end(), 0.0, 1.0); // treat disabled filtering as 100% FDR + sort(XL_FDR.begin(), XL_FDR.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters + for (double xlFDR : XL_FDR) + { + + if (xlFDR > 0.0 && xlFDR < 1.0) + { + IDFilter::filterHitsByScore(xl_pi, xlFDR); + } + { + String out2(out_idxml); + out2.substitute(".idXML", "_perc_"); + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); + IdXMLFile().store(out2 + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); + } + } } } else From 3ba93a35cbbf956ffa7828515591c8173e6535bb Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 19 Feb 2020 10:15:11 +0100 Subject: [PATCH 100/471] extended SSE to add mass errors --- src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index c6e9b94b405..42cd1589ac0 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -266,12 +266,13 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, { if (!annotated_hits[scan_index].empty()) { + const MSSpectrum& spec = exp[scan_index]; // create empty PeptideIdentification object and fill meta data PeptideIdentification pi{}; + pi.setMetaValue("spectrum_reference", spec.getNativeID()); pi.setMetaValue("scan_index", static_cast(scan_index)); pi.setScoreType("hyperscore"); pi.setHigherScoreBetter(true); - const MSSpectrum& spec = exp[scan_index]; double mz = spec.getPrecursors()[0].getMZ(); pi.setRT(spec.getRT()); pi.setMZ(mz); From 07c8a06e8604eaca0c5c7b99f14d83128588ba72 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 3 Mar 2020 09:35:00 +0100 Subject: [PATCH 101/471] compile time enable/disable quantile annotations --- src/utils/OpenNuXL.cpp | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 4c80964a002..4c4fee4da72 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -126,7 +126,9 @@ using namespace boost::accumulators; //#define FILTER_RANKS 1 //#define CALCULATE_NUCLEOTIDE_TAGS 1 +#ifdef ANNOTATED_QUANTILES typedef accumulator_set > quantile_accu_t; +#endif using namespace OpenMS; using namespace OpenMS::Internal; @@ -4071,8 +4073,11 @@ static void scoreXLIons_( vector annotated_peptides_lock(annotated_peptides.size()); for (size_t i = 0; i != annotated_peptides_lock.size(); i++) { omp_init_lock(&(annotated_peptides_lock[i])); } #endif + +#ifdef ANNOTATED_QUANTILES vector annotated_peptides_quantiles_peptides(spectra.size(), quantile_accu_t(quantile_probability = 0.95)); vector annotated_peptides_quantiles_XLs(spectra.size(), quantile_accu_t(quantile_probability = 0.95)); +#endif // load fasta file progresslogger.startProgress(0, 1, "Load database from FASTA file..."); @@ -4367,7 +4372,9 @@ static void scoreXLIons_( omp_set_lock(&(annotated_peptides_lock[scan_index])); #endif { +#ifdef ANNOTATED_QUANTILES annotated_peptides_quantiles_peptides[scan_index](ah.total_loss_score); +#endif annotated_peptides[scan_index].emplace_back(move(ah)); // prevent vector from growing indefinitly (memory) but don't shrink the vector every time @@ -4603,7 +4610,9 @@ static void scoreXLIons_( omp_set_lock(&(annotated_XLs_lock[scan_index])); #endif { +#ifdef ANNOTATED_QUANTILES annotated_peptides_quantiles_XLs[scan_index](ah.total_loss_score + ah.partial_loss_score); +#endif annotated_XLs[scan_index].emplace_back(move(ah)); // prevent vector from growing indefinitly (memory) but don't shrink the vector every time @@ -4772,7 +4781,8 @@ static void scoreXLIons_( // annotate RNPxl related information to hits and create report vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); -/* + +#ifdef ANNOTATED_QUANTILES for (Size scan_index = 0; scan_index != peptide_ids.size(); ++scan_index) { PeptideIdentification& pi = peptide_ids[scan_index]; @@ -4789,7 +4799,7 @@ static void scoreXLIons_( } } } -*/ +#endif From 1e79361ec814bd38700cd643a03cf524918f1263 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 10 Mar 2020 11:40:17 +0100 Subject: [PATCH 102/471] reenable partial loss filtering --- src/utils/OpenNuXL.cpp | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 4c4fee4da72..1c7392c48c4 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -571,12 +571,19 @@ class OpenNuXL : static bool badPartialLossScore(float tlss_Morph, float plss_Morph, float plss_MIC, float plss_im_MIC, float plss_pc_MIC, float marker_ions_score) { +#if !defined DONT_ACCUMULATE_PARTIAL_ION_SCORES + // if partial loss scores accumulate on the total loss scores, we first need to calculate the individual components + plss_Morph -= tlss_Morph; + float tlss_MIC = tlss_Morph - static_cast(tlss_Morph); + plss_MIC -= tlss_MIC; +#endif + if (plss_Morph + tlss_Morph < 5.03) return true; // less than 5 peaks? 3% TIC if (plss_MIC + plss_im_MIC + plss_pc_MIC + marker_ions_score < 0.03) return true; // if we don't see shifted ladder ions, we need at least some signal in the shifted immonium ions - return (plss_Morph < MIN_SHIFTED_IONS && plss_im_MIC < 0.03); + return (plss_Morph < MIN_SHIFTED_IONS && plss_im_MIC < 0.03); } @@ -4436,9 +4443,9 @@ static void scoreXLIons_( { const Size & scan_index = l->second.first; const PeakSpectrum & exp_spectrum = spectra[scan_index]; -/////////////////////////////////////////////////////////////////////////// basically an ID-filter reimplementation + ////////////////////////////////////////// + // ID-Filter if (skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) { continue; } -////////////////////////////////////////// #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } @@ -4498,6 +4505,12 @@ static void scoreXLIons_( vector intensity_xls(total_loss_template_z1_b_ions.size(), 0.0); +#ifdef DONT_ACCUMULATE_PARTIAL_ION_SCORES + std::fill(b_ions.begin(), b_ions.end(), 0); + std::fill(y_ions.begin(), y_ions.end(), 0); +#endif + vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); + float plss_MIC(0), plss_err(1.0), plss_Morph(0), From 6178a3b45d2a5d00a49f5cd504921b0fa826313f Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 12 Mar 2020 10:10:32 +0100 Subject: [PATCH 103/471] fix autotune and idfilter combination --- src/utils/OpenNuXL.cpp | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1c7392c48c4..3bc6c5b4494 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -3830,7 +3830,7 @@ static void scoreXLIons_( // autotune (only works if non-XL peptides present) set skip_peptide_spectrum; - if (autotune) + if (autotune || idfilter) { SimpleSearchEngineAlgorithm sse; vector prot_ids; @@ -3897,11 +3897,14 @@ static void scoreXLIons_( // use 68-percentile as in identipy double new_fragment_mass_tolerance = 4.0 * median_fragment_error_ppm[median_fragment_error_ppm.size() * 0.68]; - fragment_mass_tolerance = new_fragment_mass_tolerance; // set new fragment mass tolerance double left_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.005]; double median_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.5]; double right_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.995]; + if (autotune) + { + fragment_mass_tolerance = new_fragment_mass_tolerance; // set new fragment mass tolerance + } cout << "New fragment mass tolerance (ppm): " << new_fragment_mass_tolerance << endl; cout << "Estimated precursor mass tolerance (ppm): " << left_precursor_mass_tolerance << "\t" << median_precursor_mass_tolerance << "\t" << right_precursor_mass_tolerance << endl; } @@ -4509,8 +4512,6 @@ static void scoreXLIons_( std::fill(b_ions.begin(), b_ions.end(), 0); std::fill(y_ions.begin(), y_ions.end(), 0); #endif - vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); - float plss_MIC(0), plss_err(1.0), plss_Morph(0), From af5ffa12e9336626014abf91d181b8abdbc708a0 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 13 Mar 2020 09:18:30 +0100 Subject: [PATCH 104/471] use percolator in IDFilter --- src/utils/OpenNuXL.cpp | 80 ++++++++++++++++++++++++++++++++++-------- 1 file changed, 66 insertions(+), 14 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 3bc6c5b4494..e8e7b08a10a 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -125,6 +125,7 @@ using namespace boost::accumulators; //#define SVM_RECALIBRATE //#define FILTER_RANKS 1 //#define CALCULATE_NUCLEOTIDE_TAGS 1 +//#define DONT_ACCUMULATE_PARTIAL_ION_SCORES 1 #ifdef ANNOTATED_QUANTILES typedef accumulator_set > quantile_accu_t; @@ -3799,6 +3800,7 @@ static void scoreXLIons_( ProgressLogger progresslogger; progresslogger.setLogType(log_type_); + // Parameter: Input FileHandler fh; FileTypes::Type in_type = fh.getType(getStringOption_("in")); @@ -3812,9 +3814,10 @@ static void scoreXLIons_( in_mzml = convertRawFile_(getStringOption_("in")); } + String out_idxml = getStringOption_("out"); String in_db = getStringOption_("database"); - + // Int min_precursor_charge = getIntOption_("precursor:min_charge"); Int max_precursor_charge = getIntOption_("precursor:max_charge"); double precursor_mass_tolerance = getDoubleOption_("precursor:mass_tolerance"); @@ -3858,23 +3861,73 @@ static void scoreXLIons_( cout << "Running autotune..." << endl; sse.search(in_mzml, in_db, prot_ids, pep_ids); - cout << "Calculating FDR..." << endl; - FalseDiscoveryRate fdr; - fdr.apply(pep_ids); - cout << "Filtering ..." << endl; - IDFilter::filterHitsByScore(pep_ids, 0.01); // 1% PSM-FDR - IDFilter::removeEmptyIdentifications(pep_ids); - cout << "Peptide identifications left: " << pep_ids.size() << endl; +/// try to run percolator + { + vector perc_prot_ids; + vector perc_pep_ids; - // ID-filter part for linear peptides - if (idfilter) - { - for (const auto& pi : pep_ids) + const String percolator_executable = getStringOption_("percolator_executable"); + bool sufficient_PSMs_for_score_recalibration = pep_ids.size() > 1000; + if (!percolator_executable.empty() && sufficient_PSMs_for_score_recalibration) // only try to call percolator if we have some PSMs + { + // run percolator on idXML + String perc_out = out_idxml; + perc_out.substitute(".idXML", "_sse_perc.idXML"); +// String weights_out = out_idxml; +// weights_out.substitute(".idXML", "_sse.weights"); + + QStringList process_params; + process_params << "-in" << out_idxml.toQString() + << "-out" << perc_out.toQString() + << "-percolator_executable" << percolator_executable.toQString() + << "-train-best-positive" + << "-score_type" << "q-value" + << "-post-processing-tdc"; +// << "-nested-xval-bins" << "3" + //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice +// << "-weights" << weights_out.toQString(); + ; + TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); + + if (exit_code != EXECUTION_OK) + { + OPENMS_LOG_WARN << "Score recalibration failed in IDFilter. Using original results." << endl; + } + else + { + // load back idXML + IdXMLFile().load(perc_out, perc_prot_ids, perc_pep_ids); + + // generate filtered results + IDFilter::keepNBestHits(perc_pep_ids, 1); + IDFilter::removeUnreferencedProteins(perc_prot_ids, perc_pep_ids); + } + } + + cout << "Filtering ..." << endl; + IDFilter::filterHitsByScore(perc_pep_ids, 0.01); // 1% PSM-FDR + IDFilter::removeEmptyIdentifications(perc_pep_ids); + cout << "Peptide PSMs at 1% FDR: " << perc_pep_ids.size() << endl; + + // ID-filter part for linear peptides + if (idfilter) { - skip_peptide_spectrum.insert((String)pi.getMetaValue("spectrum_reference")); // get native id + for (const auto& pi : perc_pep_ids) + { + skip_peptide_spectrum.insert((String)pi.getMetaValue("spectrum_reference")); // get native id + } } } +////////// end percolator part + cout << "Calculating FDR..." << endl; + FalseDiscoveryRate fdr; + fdr.apply(pep_ids); + cout << "Filtering ..." << endl; + IDFilter::filterHitsByScore(pep_ids, 0.01); // 1% PSM-FDR + IDFilter::removeEmptyIdentifications(pep_ids); + cout << "Peptide PSMs at 1% FDR (no percolator): " << pep_ids.size() << endl; + if (pep_ids.size() > 100) { vector median_fragment_error_ppm; @@ -3916,7 +3969,6 @@ static void scoreXLIons_( OPENMS_LOG_INFO << "IDFilter excludes " << skip_peptide_spectrum.size() << " spectra." << endl; - String out_idxml = getStringOption_("out"); String out_tsv = getStringOption_("out_tsv"); fast_scoring_ = getStringOption_("RNPxl:scoring") == "fast" ? true : false; From 3ab783068e76b73cf381d12bcde1e493be4a2360 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 21 Apr 2020 13:19:53 +0200 Subject: [PATCH 105/471] write pin file --- src/utils/OpenNuXL.cpp | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 4781febcaec..28a34963444 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -716,7 +716,7 @@ class OpenNuXL : OPENMS_PRECONDITION(intensity_sum.size() == b_ions.size(), "Sum array needs to be of same size as b-ion array"); OPENMS_PRECONDITION(intensity_sum.size() == y_ions.size(), "Sum array needs to be of same size as y-ion array"); OPENMS_PRECONDITION(peak_matched.size() == exp_spectrum.size(), "Peak matched needs to be of same size as experimental spectrum"); - OPENMS_PRECONDITION(std::count_if(peak_matched.begin(), peak_matched.end(), [](bool b){return b == true;}) == 0;, "Peak matched must be initialized to false"); + OPENMS_PRECONDITION(std::count_if(peak_matched.begin(), peak_matched.end(), [](bool b){return b == true;}) == 0, "Peak matched must be initialized to false"); double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); @@ -4779,8 +4779,8 @@ static void scoreXLIons_( progresslogger.startProgress(0, 1, "localization..."); - assert(exp.size() == annotated_XLss.size()); - assert(exp.size() == annotated_peptides.size()); + assert(spectra.size() == annotated_XLs.size()); + assert(spectra.size() == annotated_peptides.size()); // remove all but top n scoring for localization (usually all but the first one) filterTopNAnnotations_(annotated_XLs, report_top_hits); @@ -5452,6 +5452,8 @@ variable_modifications -0.0944707 perc_out.substitute(".idXML", "_perc.idXML"); String weights_out = out_idxml; weights_out.substitute(".idXML", ".weights"); + String pin = out_idxml; + pin.substitute(".idXML", ".tsv"); QStringList process_params; process_params << "-in" << out_idxml.toQString() @@ -5463,11 +5465,10 @@ variable_modifications -0.0944707 << "-post-processing-tdc" // << "-nested-xval-bins" << "3" //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice - << "-weights" << weights_out.toQString(); -#if DEBUG_OpenNuXL - process_params << "-out_pout_target" << "merged_target.tab" << "-out_pout_decoy" << "merged_decoy.tab"; -#endif - ; + << "-weights" << weights_out.toQString() + << "-out_pin" << pin.toQString(); +// process_params << "-out_pout_target" << "merged_target.tab" << "-out_pout_decoy" << "merged_decoy.tab"; + TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); if (exit_code != EXECUTION_OK) From 90d9607eeb7bc6ff42fe69865019211892ff27b3 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 21 Apr 2020 16:48:48 +0200 Subject: [PATCH 106/471] [NOP] fixed some style issues --- src/utils/OpenNuXL.cpp | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 28a34963444..8291891c133 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -428,7 +428,7 @@ class OpenNuXL : setValidFormats_("out_tsv", ListUtils::create("tsv")); registerTOPPSubsection_("precursor", "Precursor (Parent Ion) Options"); - registerDoubleOption_("precursor:mass_tolerance", "", 6.0, "Precursor mass tolerance (+/- around precursor m/z)", false); + registerDoubleOption_("precursor:mass_tolerance", "", 6.0, "Precursor mass tolerance (+/- around precursor m/z).", false); StringList precursor_mass_tolerance_unit_valid_strings; precursor_mass_tolerance_unit_valid_strings.emplace_back("ppm"); @@ -442,26 +442,26 @@ class OpenNuXL : // consider one before annotated monoisotopic peak and the annotated one IntList isotopes = {0}; - registerIntList_("precursor:isotopes", "", isotopes, "Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak)", false, false); + registerIntList_("precursor:isotopes", "", isotopes, "Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak).", false, false); registerTOPPSubsection_("fragment", "Fragments (Product Ion) Options"); - registerDoubleOption_("fragment:mass_tolerance", "", 20.0, "Fragment mass tolerance (+/- around fragment m/z)", false); + registerDoubleOption_("fragment:mass_tolerance", "", 20.0, "Fragment mass tolerance (+/- around fragment m/z).", false); StringList fragment_mass_tolerance_unit_valid_strings; fragment_mass_tolerance_unit_valid_strings.emplace_back("ppm"); fragment_mass_tolerance_unit_valid_strings.emplace_back("Da"); - registerStringOption_("fragment:mass_tolerance_unit", "", "ppm", "Unit of fragment m", false, false); + registerStringOption_("fragment:mass_tolerance_unit", "", "ppm", "Unit of fragment mass tolerance.", false, false); setValidStrings_("fragment:mass_tolerance_unit", fragment_mass_tolerance_unit_valid_strings); registerTOPPSubsection_("modifications", "Modifications Options"); vector all_mods; ModificationsDB::getInstance()->getAllSearchModifications(all_mods); - registerStringList_("modifications:fixed", "", ListUtils::create(""), "Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'", false); + registerStringList_("modifications:fixed", "", ListUtils::create(""), "Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'.", false); setValidStrings_("modifications:fixed", all_mods); registerStringList_("modifications:variable", "", ListUtils::create("Oxidation (M)"), "Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'", false); setValidStrings_("modifications:variable", all_mods); - registerIntOption_("modifications:variable_max_per_peptide", "", 2, "Maximum number of residues carrying a variable modification per candidate peptide", false, false); + registerIntOption_("modifications:variable_max_per_peptide", "", 2, "Maximum number of residues carrying a variable modification per candidate peptide.", false, false); registerTOPPSubsection_("peptide", "Peptide Options"); registerIntOption_("peptide:min_size", "", 6, "Minimum size a peptide must have after digestion to be considered in the search.", false, true); @@ -492,23 +492,23 @@ class OpenNuXL : registerTOPPSubsection_("RNPxl", "RNPxl Options"); registerIntOption_("RNPxl:length", "", 2, "Oligonucleotide maximum length. 0 = disable search for NA variants.", false); - registerStringOption_("RNPxl:sequence", "", "", "Sequence to restrict the generation of oligonucleotide chains. (disabled for empty sequence)", false); + registerStringOption_("RNPxl:sequence", "", "", "Sequence to restrict the generation of oligonucleotide chains. (disabled for empty sequence).", false); registerStringList_("RNPxl:target_nucleotides", "", {"A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"}, - "format: target nucleotide=empirical formula of nucleoside monophosphate \n e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU \n or e.g. Y=C10H14N5O7PS where Y represents tG", + "format: target nucleotide=empirical formula of nucleoside monophosphate \n e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU \n or e.g. Y=C10H14N5O7PS where Y represents tG.", false, false); registerStringList_("RNPxl:nt_groups", "", {}, - "Restrict which nucleotides can cooccur in a precursor adduct to be able to search both RNA and DNA (Formate e.g.: AU CG).", + "Restrict which nucleotides can cooccur in a precursor adduct to be able to search both RNA and DNA (format: 'AU CG').", false, false); - registerStringList_("RNPxl:mapping", "", {"A->A", "C->C", "G->G", "U->U"}, "format: source->target e.g. A->A, ..., U->U, U->X", false, false); + registerStringList_("RNPxl:mapping", "", {"A->A", "C->C", "G->G", "U->U"}, "format: source->target e.g. A->A, ..., U->U, U->X.", false, false); // define if nucleotide can cross-link (produce y,b,a,immonium-ion shifts) in addition to marker ions registerStringOption_("RNPxl:can_cross_link", @@ -537,11 +537,11 @@ class OpenNuXL : registerStringList_("RNPxl:fragment_adducts", "", fragment_adducts, - "format: [target nucleotide]:[formula] or [precursor adduct]->[fragment adduct formula];[name]: e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O->C9H11N2O8P1;U-H2O',", + "format: [target nucleotide]:[formula] or [precursor adduct]->[fragment adduct formula];[name]: e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O->C9H11N2O8P1;U-H2O'.", false, false); - registerStringList_("RNPxl:modifications", "", modifications, "format: empirical formula e.g -H2O, ..., H2O+PO3", false, false); + registerStringList_("RNPxl:modifications", "", modifications, "format: empirical formula e.g U: U:-H2O, ..., U:H2O+PO3.", false, false); registerStringOption_("RNPxl:scoring", "", "fast", "Scoring algorithm used in prescoring (fast: total-loss, slow: all losses).", false, false); setValidStrings_("RNPxl:scoring", {"fast", "slow"}); @@ -1484,7 +1484,7 @@ static void scoreXLIons_( } // De novo tagger - class OPENMS_DLLAPI OpenNuXLTagger + class OpenNuXLTagger { public: From d27ec4ca3c338845b6068a4d4322ad95a088ad69 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 5 May 2020 23:23:58 +0200 Subject: [PATCH 107/471] fix some tests --- .../ID/SimpleSearchEngineAlgorithm.cpp | 22 - .../ANALYSIS/MRM/MRMFragmentSelection.cpp | 10 +- .../source/CHEMISTRY/SpectrumAnnotator.cpp | 437 +-- .../TheoreticalSpectrumGenerator.cpp | 2 +- .../openms/data/MRMFeatureQCFile_1_test.csv | 10 +- .../openms/data/MRMFeatureQCFile_2_test.csv | 10 +- .../openms/source/SpectrumAnnotator_test.cpp | 2 +- .../TheoreticalSpectrumGenerator_test.cpp | 16 +- .../topp/IDFileConverter_22_output.idXML | 110 +- src/tests/topp/OpenNuXL_1_output.idXML | 1354 ++++++---- src/tests/topp/OpenNuXL_2_output.idXML | 1407 ++++++---- src/tests/topp/OpenNuXL_3_output.idXML | 1606 ++++++----- src/tests/topp/OpenNuXL_4_output.idXML | 2357 +++++++++++------ src/tests/topp/OpenNuXL_4_output2.tsv | 62 +- src/tests/topp/OpenNuXL_5_output.idXML | 1474 +++++++---- src/tests/topp/SimpleSearchEngine_1_out.idXML | 8 +- src/topp/IDFileConverter.cpp | 6 - src/utils/OpenNuXL.cpp | 10 +- 18 files changed, 5627 insertions(+), 3276 deletions(-) diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index 9a30ff20deb..0b066776146 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -468,27 +468,6 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, digestor.setMissedCleavages(0); startProgress(0, 1, "Generate decoys..."); -<<<<<<< HEAD - // append decoy proteins - const size_t old_size = fasta_db.size(); - for (size_t i = 0; i != old_size; ++i) - { - FASTAFile::FASTAEntry e = fasta_db[i]; - - std::vector output; - digestor.digest(AASequence::fromString(e.sequence), output); - - // pseudo reverse protein digest - e.sequence = ""; - for (const auto & aas : output) - { - std::string s = aas.toUnmodifiedString(); - auto last = --s.end(); - std::reverse(s.begin(), last); - e.sequence += s; - } - -======= DecoyGenerator decoy_generator; // append decoy proteins @@ -497,7 +476,6 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, { FASTAFile::FASTAEntry e = fasta_db[i]; e.sequence = decoy_generator.reversePeptides(AASequence::fromString(e.sequence), enzyme_).toString(); ->>>>>>> upstream/develop e.identifier = "DECOY_" + e.identifier; fasta_db.push_back(e); } diff --git a/src/openms/source/ANALYSIS/MRM/MRMFragmentSelection.cpp b/src/openms/source/ANALYSIS/MRM/MRMFragmentSelection.cpp index 15c4a1cc00e..14e2f994abc 100644 --- a/src/openms/source/ANALYSIS/MRM/MRMFragmentSelection.cpp +++ b/src/openms/source/ANALYSIS/MRM/MRMFragmentSelection.cpp @@ -139,15 +139,7 @@ namespace OpenMS { if (!(name.hasSubstring("-H") || name.hasSubstring("-C") || name.hasSubstring("-N"))) { - Size c = count(name.begin(), name.end(), '+'); - if (ListUtils::contains(allowed_charges, String(c))) - { - return true; - } - else - { - return false; - } + return charges_ok; } else { diff --git a/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp b/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp index f23e35429b5..4930bcd1bde 100644 --- a/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp +++ b/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp @@ -125,279 +125,292 @@ namespace OpenMS { PeakSpectrum theoretical_spec; vector > al; - Int zmin = 1; - Int zmax = 2; + const Int zmin = 1; + const Int zmax = 2; tg.getSpectrum(theoretical_spec, ph.getSequence(), zmin, min(ph.getCharge(), zmax)); OPENMS_PRECONDITION(theoretical_spec.isSorted(), "TheoreticalSpectrumGenerator::getSpectrum did not yield a sorted spectrum!") - if (!spec.isSorted()) - { - spec.sortByPosition(); - } + if (!spec.isSorted()) { spec.sortByPosition(); } sa.getSpectrumAlignment(al, theoretical_spec, spec); // peaks from theor. may be matched to none or one in spec! - PeakSpectrum::StringDataArray theo_annot = theoretical_spec.getStringDataArrays().front(); - PeakSpectrum::StringDataArray type_annotations = PeakSpectrum::StringDataArray(); - PeakSpectrum::FloatDataArray error_annotations = PeakSpectrum::FloatDataArray(); - type_annotations.setName("IonName"); + PeakSpectrum::FloatDataArray error_annotations; error_annotations.setName("IonMatchError"); - type_annotations.resize(spec.size()); error_annotations.resize(spec.size()); - for (vector >::const_iterator it = al.begin(); it != al.end(); ++it) + + PeakSpectrum::StringDataArray type_annotations; + type_annotations.setName("IonNames"); + type_annotations.resize(spec.size()); + + PeakSpectrum::IntegerDataArray charge_annotations; + charge_annotations.setName("Charges"); + charge_annotations.resize(spec.size()); + + for (auto it = al.begin(); it != al.end(); ++it) { - error_annotations[it->second] = std::fabs(spec[it->second].getMZ() - theoretical_spec[it->first].getMZ()); - type_annotations[it->second] = theo_annot[it->first]; + error_annotations[it->second] = std::fabs(spec[it->second].getMZ() - theoretical_spec[it->first].getMZ()); + type_annotations[it->second] = theoretical_spec.getStringDataArrays()[0][it->first]; + charge_annotations[it->second] = theoretical_spec.getIntegerDataArrays()[0][it->first]; } + Param sap = sa.getParameters(); spec.setMetaValue("fragment_mass_tolerance", sap.getValue("tolerance")); spec.setMetaValue("fragment_mass_tolerance_ppm", false); - spec.setStringDataArrays(PeakSpectrum::StringDataArrays(1, type_annotations)); - spec.setFloatDataArrays(PeakSpectrum::FloatDataArrays(1, error_annotations)); + spec.setFloatDataArrays(PeakSpectrum::FloatDataArrays(1, std::move(error_annotations))); + spec.setStringDataArrays(PeakSpectrum::StringDataArrays(1, std::move(type_annotations))); + spec.setIntegerDataArrays(PeakSpectrum::IntegerDataArrays(1, std::move(charge_annotations))); } void SpectrumAnnotator::addIonMatchStatistics(PeptideIdentification& pi, MSSpectrum& spec, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const { - if (!spec.empty()) + if (spec.empty()) return; + + for (auto ph = pi.getHits().begin(); ph != pi.getHits().end(); ++ph) { - for (vector::iterator ph = pi.getHits().begin(); ph != pi.getHits().end(); ++ph) + annotateMatches(spec, *ph, tg, sa); + + spec.sortByIntensity(); + + StringList ions; + double sum_intensity = 0; + double match_intensity = 0; + vector fragmenterrors, intensities, mzs; // sorted by ascending intensity via spec.sortByIntensity for topN statistics + fragmenterrors.reserve(spec.size()); + intensities.reserve(spec.size()); + mzs.reserve(spec.size()); + + double nint = 0; + double cint = 0; + + StringList allowed_types = ListUtils::create("y,b,a,c,x,z"); + map > ion_series; + for (StringList::iterator st = allowed_types.begin(); st != allowed_types.end(); ++st) { - annotateMatches(spec, *ph, tg, sa); - spec.sortByIntensity(); - - StringList ions; - double sum_intensity = 0; - double match_intensity = 0; - vector fragmenterrors, intensities, mzs; // sorted by ascending intensity via spec.sortByIntensity for topN statistics - fragmenterrors.reserve(spec.size()); - intensities.reserve(spec.size()); - mzs.reserve(spec.size()); - - double nint = 0; - double cint = 0; - - StringList allowed_types = ListUtils::create("y,b,a,c,x,z"); - map > ion_series; - for (StringList::iterator st = allowed_types.begin(); st != allowed_types.end(); ++st) - { - ion_series.insert(make_pair(*st, vector(ph->getSequence().size()-1, false))); - } + ion_series.insert(make_pair(*st, vector(ph->getSequence().size()-1, false))); + } + + PeakSpectrum::StringDataArray type_annotations; + PeakSpectrum::FloatDataArray error_annotations; + PeakSpectrum::IntegerDataArray charge_annotations; + + for (auto it = spec.getStringDataArrays().begin(); it != spec.getStringDataArrays().end(); ++it) + { + if (it->getName() == "IonNames") { type_annotations = *it; break; } + } + for (auto it = spec.getFloatDataArrays().begin(); it != spec.getFloatDataArrays().end(); ++it) + { + if (it->getName() == "IonMatchError") { error_annotations = *it; break; } + } + for (auto it = spec.getIntegerDataArrays().begin(); it != spec.getIntegerDataArrays().end(); ++it) + { + if (it->getName() == "Charges") { charge_annotations = *it; break; } + } - PeakSpectrum::StringDataArray type_annotations = PeakSpectrum::StringDataArray(); - PeakSpectrum::FloatDataArray error_annotations = PeakSpectrum::FloatDataArray(); - for (PeakSpectrum::StringDataArrays::iterator it = spec.getStringDataArrays().begin(); it != spec.getStringDataArrays().end(); ++it) + for (size_t i = 0; i < spec.size(); ++i) + { + sum_intensity += spec[i].getIntensity(); + String ion_name = type_annotations.at(i); + if (ion_name.empty()) continue; + + fragmenterrors.push_back(error_annotations.at(i)); + intensities.push_back(spec[i].getIntensity()); + match_intensity += spec[i].getIntensity(); + mzs.push_back(spec[i].getMZ()); + if (charge_annotations.size() == type_annotations.size()) { - if (it->getName() == "IonName") - type_annotations = *it; + ion_name += String(charge_annotations[i], '+'); } - for (PeakSpectrum::FloatDataArrays::iterator it = spec.getFloatDataArrays().begin(); it != spec.getFloatDataArrays().end(); ++it) + + if (terminal_series_match_ratio_) { - if (it->getName() == "IonMatchError") - error_annotations = *it; + if (boost::regex_match(ion_name, nt_regex_)) + { + nint += spec[i].getIntensity(); + } + else if (boost::regex_match(ion_name, ct_regex_)) + { + cint += spec[i].getIntensity(); + } } - for (size_t i = 0; i < spec.size(); ++i) + if (max_series_) // without loss max series is sometimes pretty crummy { - sum_intensity += spec[i].getIntensity(); - if (!type_annotations.at(i).empty()) // implies error_annotations is set, too. + const String& ion_type = ion_name.prefix(1); + boost::cmatch what; + if (boost::regex_match(ion_name.c_str(), what, seriesposition_regex_) && + ListUtils::contains(allowed_types, ion_type)) { - fragmenterrors.push_back(error_annotations.at(i)); - intensities.push_back(spec[i].getIntensity()); - match_intensity += spec[i].getIntensity(); - mzs.push_back(spec[i].getMZ()); - const String& ion_name = type_annotations.at(i); + // what[0] contains the whole string + // what[1] contains the response code + try + { + int i = std::atoi(what[1].first); + ion_series[ion_type].at(i-1) = true; + } + catch (std::out_of_range&) { - ions.push_back(ion_name); - if (terminal_series_match_ratio_) - { - if (boost::regex_match(ion_name, nt_regex_)) - { - nint += spec[i].getIntensity(); - } - else if (boost::regex_match(ion_name, ct_regex_)) - { - cint += spec[i].getIntensity(); - } - } - if (max_series_) // without loss max series is sometimes pretty crummy - { - const String& ion_type = ion_name.prefix(1); - boost::cmatch what; - if (boost::regex_match(ion_name.c_str(), what, seriesposition_regex_) && - ListUtils::contains(allowed_types, ion_type)) - { - // what[0] contains the whole string - // what[1] contains the response code - try - { - int i = std::atoi(what[1].first); - ion_series[ion_type].at(i-1) = true; - } - catch (std::out_of_range&) - { - OPENMS_LOG_WARN << "Note: Ions of " << ion_type << ion_name.substr(1).remove('+').toInt() - << " will be ignored for max_series " << ph->getSequence().toString() << endl; - continue; - } - } - } + OPENMS_LOG_WARN << "Note: Ions of " << ion_type << ion_name.substr(1).remove('+').toInt() + << " will be ignored for max_series " << ph->getSequence().toString() << endl; + continue; } } } - if (basic_statistics_) - { - ph->setMetaValue("matched_ions", ListUtils::concatenate(ions, ",")); - ph->setMetaValue("matched_intensity", match_intensity); - ph->setMetaValue("matched_ion_number", ions.size()); - ph->setMetaValue("peak_number", spec.size()); - ph->setMetaValue("sum_intensity", sum_intensity); - } - if (terminal_series_match_ratio_) + ions.emplace_back(std::move(ion_name)); + } + if (basic_statistics_) + { + ph->setMetaValue("matched_ions", ListUtils::concatenate(ions, ",")); + ph->setMetaValue("matched_intensity", match_intensity); + ph->setMetaValue("matched_ion_number", ions.size()); + ph->setMetaValue("peak_number", spec.size()); + ph->setMetaValue("sum_intensity", sum_intensity); + } + if (terminal_series_match_ratio_) + { + ph->setMetaValue("NTermIonCurrentRatio", nint/match_intensity); + ph->setMetaValue("CTermIonCurrentRatio", cint/match_intensity); + } + if (topNmatch_fragmenterrors_) + { + if (fragmenterrors.empty()) { - ph->setMetaValue("NTermIonCurrentRatio", nint/match_intensity); - ph->setMetaValue("CTermIonCurrentRatio", cint/match_intensity); + ph->setMetaValue("median_fragment_error", 0); + ph->setMetaValue("IQR_fragment_error", 0); + ph->setMetaValue("topN_meanfragmenterror", 0); + ph->setMetaValue("topN_MSEfragmenterror", 0); + ph->setMetaValue("topN_stddevfragmenterror", 0); } - if (topNmatch_fragmenterrors_) + else { - if (fragmenterrors.empty()) + vector fe(fragmenterrors); + std::size_t mid = fe.size() / 2; + std::size_t lq = fe.size() / 4; + std::size_t uq = lq + mid; + std::nth_element(fe.begin(), fe.begin()+mid, fe.end()); + if (fe.size() % 2 != 0) { - ph->setMetaValue("median_fragment_error", 0); - ph->setMetaValue("IQR_fragment_error", 0); - ph->setMetaValue("topN_meanfragmenterror", 0); - ph->setMetaValue("topN_MSEfragmenterror", 0); - ph->setMetaValue("topN_stddevfragmenterror", 0); + ph->setMetaValue("median_fragment_error", fe[mid]); } else { - vector fe(fragmenterrors); - std::size_t mid = fe.size() / 2; - std::size_t lq = fe.size() / 4; - std::size_t uq = lq + mid; - std::nth_element(fe.begin(), fe.begin()+mid, fe.end()); - if (fe.size() % 2 != 0) - { - ph->setMetaValue("median_fragment_error", fe[mid]); - } - else - { - double right2mid = fe[mid]; - std::nth_element(fe.begin(), fe.begin() + mid-1, fe.end()); - ph->setMetaValue("median_fragment_error", (right2mid + fe[mid-1]) / 2.0); - } - std::nth_element(fe.begin(), fe.begin() + lq, fe.end()); - std::nth_element(fe.begin() + lq + 1, fe.begin() + mid, fe.end()); - std::nth_element(fe.begin() + mid + 1, fe.begin() + uq, fe.end()); - ph->setMetaValue("IQR_fragment_error", fe[uq]-fe[lq]); + double right2mid = fe[mid]; + std::nth_element(fe.begin(), fe.begin() + mid-1, fe.end()); + ph->setMetaValue("median_fragment_error", (right2mid + fe[mid-1]) / 2.0); + } + std::nth_element(fe.begin(), fe.begin() + lq, fe.end()); + std::nth_element(fe.begin() + lq + 1, fe.begin() + mid, fe.end()); + std::nth_element(fe.begin() + mid + 1, fe.begin() + uq, fe.end()); + ph->setMetaValue("IQR_fragment_error", fe[uq]-fe[lq]); - vector topn_fe; - topn_fe.resize(fragmenterrors.size()); - std::reverse_copy(fragmenterrors.begin(), fragmenterrors.end(), topn_fe.begin()); // fragmenterrors is sortByIntensity before, get TopN from the back of the vector - topn_fe.resize(topNmatch_fragmenterrors_); + vector topn_fe; + topn_fe.resize(fragmenterrors.size()); + std::reverse_copy(fragmenterrors.begin(), fragmenterrors.end(), topn_fe.begin()); // fragmenterrors is sortByIntensity before, get TopN from the back of the vector + topn_fe.resize(topNmatch_fragmenterrors_); - double mean = Math::mean(topn_fe.begin(), topn_fe.end()); - double stdev = Math::sd(topn_fe.begin(), topn_fe.end(), mean); + double mean = Math::mean(topn_fe.begin(), topn_fe.end()); + double stdev = Math::sd(topn_fe.begin(), topn_fe.end(), mean); - double sq_sum = 0; - for (std::vector::iterator it = topn_fe.begin(); it != topn_fe.end(); ++it) - { - sq_sum += *it * *it; - } - double m_sq_sum = (sq_sum / topn_fe.size()); - - ph->setMetaValue("topN_meanfragmenterror", mean); - ph->setMetaValue("topN_MSEfragmenterror", m_sq_sum); - ph->setMetaValue("topN_stddevfragmenterror", stdev); + double sq_sum = 0; + for (std::vector::iterator it = topn_fe.begin(); it != topn_fe.end(); ++it) + { + sq_sum += *it * *it; } + double m_sq_sum = (sq_sum / topn_fe.size()); + + ph->setMetaValue("topN_meanfragmenterror", mean); + ph->setMetaValue("topN_MSEfragmenterror", m_sq_sum); + ph->setMetaValue("topN_stddevfragmenterror", stdev); } - if (max_series_) + } + if (max_series_) + { + String max_series; + int max_stretch = 0; + for (map >::iterator tt = ion_series.begin(); tt != ion_series.end(); ++tt) { - String max_series; - int max_stretch = 0; - for (map >::iterator tt = ion_series.begin(); tt != ion_series.end(); ++tt) + int stretch = 0; + for (vector::iterator it = tt->second.begin(); it != tt->second.end(); ++it) { - int stretch = 0; - for (vector::iterator it = tt->second.begin(); it != tt->second.end(); ++it) + if (*it) + { + ++stretch; + } + else + { + stretch = 0; + } + if (stretch > max_stretch) { - if (*it) - { - ++stretch; - } - else - { - stretch = 0; - } - if (stretch > max_stretch) - { - max_stretch = stretch; - max_series = tt->first; - } + max_stretch = stretch; + max_series = tt->first; } } - ph->setMetaValue("max_series_type", max_series); - ph->setMetaValue("max_series_size", max_stretch); } - //TODO parent peak intensity complement pairs number - if (SN_statistics_) + ph->setMetaValue("max_series_type", max_series); + ph->setMetaValue("max_series_size", max_stretch); + } + //TODO parent peak intensity complement pairs number + if (SN_statistics_) + { + float sn_by_matched_intensity = (match_intensity / ions.size()) / + ((sum_intensity-match_intensity) / (spec.size()-ions.size())); + if (spec.size() - ions.size() == 0) { - float sn_by_matched_intensity = (match_intensity / ions.size()) / - ((sum_intensity-match_intensity) / (spec.size()-ions.size())); - if (spec.size() - ions.size() == 0) - { - sn_by_matched_intensity = 0; - } - ph->setMetaValue("sn_by_matched_intensity", sn_by_matched_intensity); + sn_by_matched_intensity = 0; + } + ph->setMetaValue("sn_by_matched_intensity", sn_by_matched_intensity); - float median = 0; - // spec is already in sorted order of intensity - if (spec.size() % 2 == 0) - median = (spec[spec.size() / 2 - 1].getIntensity() + spec[spec.size() / 2].getIntensity()) / 2; - else - median = spec[spec.size() / 2].getIntensity(); - float sign_int= 0; - float nois_int = 0; - size_t sign_count= 0; - size_t nois_count = 0; - for (MSSpectrum::const_iterator pt = spec.begin(); pt != spec.end(); ++pt) + float median = 0; + // spec is already in sorted order of intensity + if (spec.size() % 2 == 0) + median = (spec[spec.size() / 2 - 1].getIntensity() + spec[spec.size() / 2].getIntensity()) / 2; + else + median = spec[spec.size() / 2].getIntensity(); + float sign_int= 0; + float nois_int = 0; + size_t sign_count= 0; + size_t nois_count = 0; + for (MSSpectrum::const_iterator pt = spec.begin(); pt != spec.end(); ++pt) + { + if (pt->getIntensity() <= median) { - if (pt->getIntensity() <= median) - { - ++nois_count; - nois_int += pt->getIntensity(); - } - else - { - ++sign_count; - sign_int += pt->getIntensity(); - } + ++nois_count; + nois_int += pt->getIntensity(); } - float sn_by_median_intensity = (sign_int / sign_count) / (nois_int / nois_count); - if (nois_count == 0 || sign_count == 0) + else { - sn_by_median_intensity = 0; + ++sign_count; + sign_int += pt->getIntensity(); } - ph->setMetaValue("sn_by_median_intensity", sn_by_median_intensity); } - //TODO charge related features might be worth looking at in the future - if (precursor_statistics_) + float sn_by_median_intensity = (sign_int / sign_count) / (nois_int / nois_count); + if (nois_count == 0 || sign_count == 0) + { + sn_by_median_intensity = 0; + } + ph->setMetaValue("sn_by_median_intensity", sn_by_median_intensity); + } + //TODO charge related features might be worth looking at in the future + if (precursor_statistics_) + { + bool precursor = false; + for (std::vector::const_iterator pit = spec.getPrecursors().begin(); pit != spec.getPrecursors().end(); ++pit) { - bool precursor = false; - for (std::vector::const_iterator pit = spec.getPrecursors().begin(); pit != spec.getPrecursors().end(); ++pit) + spec.sortByPosition(); + //TODO what about precursor_H2O_loss and precursor_NH3_loss + if (spec.findNearest(pit->getMZ(),sa.getParameters().getValue("tolerance"), + sa.getParameters().getValue("tolerance")) > -1) { - spec.sortByPosition(); - //TODO what about precursor_H2O_loss and precursor_NH3_loss - if (spec.findNearest(pit->getMZ(),sa.getParameters().getValue("tolerance"), - sa.getParameters().getValue("tolerance")) > -1) - { - precursor = true; - } + precursor = true; } - ph->setMetaValue("precursor_in_ms2", precursor); } - //TODO add "FragmentArray"s - - Param sap = sa.getParameters(); - pi.setMetaValue("fragment_match_tolerance", sap.getValue("tolerance")); + ph->setMetaValue("precursor_in_ms2", precursor); } + //TODO add "FragmentArray"s + + Param sap = sa.getParameters(); + pi.setMetaValue("fragment_match_tolerance", sap.getValue("tolerance")); } + } void SpectrumAnnotator::updateMembers_() diff --git a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp index 7fc12eed4cc..5808b819a61 100644 --- a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp +++ b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp @@ -400,7 +400,7 @@ namespace OpenMS { const String& loss_name = losses_names[k]; // note: important to construct a string from char. If omitted it will perform pointer arithmetics on the "-" string literal - String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(ion_ordinal) + "-" + loss_name + String((Size)abs(charge), '+'); + String ion_name = String(Residue::residueTypeToIonLetter(res_type)) + String(ion_ordinal) + "-" + loss_name; ion_names.push_back(ion_name); charges.push_back(charge); } diff --git a/src/tests/class_tests/openms/data/MRMFeatureQCFile_1_test.csv b/src/tests/class_tests/openms/data/MRMFeatureQCFile_1_test.csv index 3a863cf095c..86254b1c9bf 100644 --- a/src/tests/class_tests/openms/data/MRMFeatureQCFile_1_test.csv +++ b/src/tests/class_tests/openms/data/MRMFeatureQCFile_1_test.csv @@ -1,5 +1,5 @@ -component_name,retention_time_l,retention_time_u,intensity_l,intensity_u,overall_quality_l,overall_quality_u,metaValue_peak_apex_int_l,metaValue_peak_apex_int_u,metaValue_sn_score_l,metaValue_sn_score_u -component1,1.0,2.0,1000.0,1.0e06,2.0,5.0,1000.0,1.0e06,2.0,10.0 -component2,3.0,4.0,2000.0,2.0e06,3.0,6.0,2000.0,2.0e06,5.0,20.0 -component3,5.0,6.0,3000.0,3.0e06,4.0,7.0,3000.0,3.0e06,10.0,50.0 -component4,0.0,1.0e12,0.0,1.0e12,0.0,1.0e12,0.0,1.0e12,0.0,1.0e12 +component_name,retention_time_l,retention_time_u,intensity_l,intensity_u,overall_quality_l,overall_quality_u,metaValue_peak_apex_int_l,metaValue_peak_apex_int_u,metaValue_sn_score_l,metaValue_sn_score_u +component1,1.0,2.0,1000.0,1.0e06,2.0,5.0,1000.0,1.0e06,2.0,10.0 +component2,3.0,4.0,2000.0,2.0e06,3.0,6.0,2000.0,2.0e06,5.0,20.0 +component3,5.0,6.0,3000.0,3.0e06,4.0,7.0,3000.0,3.0e06,10.0,50.0 +component4,0.0,1.0e12,0.0,1.0e12,0.0,1.0e12,0.0,1.0e12,0.0,1.0e12 diff --git a/src/tests/class_tests/openms/data/MRMFeatureQCFile_2_test.csv b/src/tests/class_tests/openms/data/MRMFeatureQCFile_2_test.csv index 143d92c9f1f..3397bf6fb74 100644 --- a/src/tests/class_tests/openms/data/MRMFeatureQCFile_2_test.csv +++ b/src/tests/class_tests/openms/data/MRMFeatureQCFile_2_test.csv @@ -1,5 +1,5 @@ -component_group_name,retention_time_l,retention_time_u,intensity_l,intensity_u,overall_quality_l,overall_quality_u,n_heavy_l,n_heavy_u,n_light_l,n_light_u,n_detecting_l,n_detecting_u,n_quantifying_l,n_quantifying_u,n_identifying_l,n_identifying_u,n_transitions_l,n_transitions_u,ion_ratio_pair_name_1,ion_ratio_pair_name_2,ion_ratio_l,ion_ratio_u,ion_ratio_feature_name,metaValue_peak_apex_int_l,metaValue_peak_apex_int_u,metaValue_sn_score_l,metaValue_sn_score_u -componentGroup1,1.0,2.0,1000.0,1.0e06,2.0,5.0,1,2,3,4,5,6,7,8,9,10,11,12,component1,component2,0.5,0.6,feature1,1000.0,1.0e06,2.0,10.0 -componentGroup2,2.0,3.0,1001.0,1.000001e06,3.0,6.0,2,3,4,5,6,7,8,9,10,11,12,13,component3,component4,1.5,1.6,feature2,1001.0,1.000001e06,5.0,20.0 -componentGroup3,3.0,4.0,1002.0,1.000002e06,4.0,7.0,3,4,5,6,7,8,9,10,11,12,13,14,component5,component6,2.5,2.6,feature3,1002.0,1.000002e06,10.0,50.0 -componentGroup5,0.0,1.0e12,0.0,1.0e12,0.0,1.0e12,0,100,0,100,0,100,0,100,0,100,0,100,,,0.0,1.0e12,,0.0,1.0e12,0.0,1.0e12 +component_group_name,retention_time_l,retention_time_u,intensity_l,intensity_u,overall_quality_l,overall_quality_u,n_heavy_l,n_heavy_u,n_light_l,n_light_u,n_detecting_l,n_detecting_u,n_quantifying_l,n_quantifying_u,n_identifying_l,n_identifying_u,n_transitions_l,n_transitions_u,ion_ratio_pair_name_1,ion_ratio_pair_name_2,ion_ratio_l,ion_ratio_u,ion_ratio_feature_name,metaValue_peak_apex_int_l,metaValue_peak_apex_int_u,metaValue_sn_score_l,metaValue_sn_score_u +componentGroup1,1.0,2.0,1000.0,1.0e06,2.0,5.0,1,2,3,4,5,6,7,8,9,10,11,12,component1,component2,0.5,0.6,feature1,1000.0,1.0e06,2.0,10.0 +componentGroup2,2.0,3.0,1001.0,1.000001e06,3.0,6.0,2,3,4,5,6,7,8,9,10,11,12,13,component3,component4,1.5,1.6,feature2,1001.0,1.000001e06,5.0,20.0 +componentGroup3,3.0,4.0,1002.0,1.000002e06,4.0,7.0,3,4,5,6,7,8,9,10,11,12,13,14,component5,component6,2.5,2.6,feature3,1002.0,1.000002e06,10.0,50.0 +componentGroup5,0.0,1.0e12,0.0,1.0e12,0.0,1.0e12,0,100,0,100,0,100,0,100,0,100,0,100,,,0.0,1.0e12,,0.0,1.0e12,0.0,1.0e12 diff --git a/src/tests/class_tests/openms/source/SpectrumAnnotator_test.cpp b/src/tests/class_tests/openms/source/SpectrumAnnotator_test.cpp index ff4aadaa3b6..cc2cb1d1612 100644 --- a/src/tests/class_tests/openms/source/SpectrumAnnotator_test.cpp +++ b/src/tests/class_tests/openms/source/SpectrumAnnotator_test.cpp @@ -115,7 +115,7 @@ START_SECTION((void SpectrumAnnotator::addIonMatchStatistics(PeptideIdentificati TEST_EQUAL(pi.getHits()[i].getMetaValue("sum_intensity"),12.1) TEST_EQUAL(pi.getHits()[i].getMetaValue("matched_ion_number"),11) TEST_EQUAL(pi.getHits()[i].getMetaValue("matched_intensity"),12.1) - TEST_STRING_EQUAL(pi.getHits()[i].getMetaValue("matched_ions"),"y1,y2,b2,y3,b3,y4,b4,y5,b5,b6,y6") + TEST_STRING_EQUAL(pi.getHits()[i].getMetaValue("matched_ions"),"y1+,y2+,b2+,y3+,b3+,y4+,b4+,y5+,b5+,b6+,y6+") TEST_STRING_EQUAL(pi.getHits()[i].getMetaValue("max_series_type"),"y") TEST_EQUAL(pi.getHits()[i].getMetaValue("max_series_size"),6) TEST_REAL_SIMILAR(pi.getHits()[i].getMetaValue("sn_by_matched_intensity"),0) diff --git a/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp b/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp index e58bb4cf6f8..7e7cbf3442a 100644 --- a/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp +++ b/src/tests/class_tests/openms/source/TheoreticalSpectrumGenerator_test.cpp @@ -833,10 +833,10 @@ START_SECTION(([EXTRA] test first prefix loss)) TEST_EQUAL(tmp.size(), 107) auto anno = tmp.getStringDataArrays()[0]; - TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1+") != anno.end(), true) - TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-H3N1+") != anno.end(), true) - TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-C1H2N2+") != anno.end(), true) - TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-C1H2N1O1+") != anno.end(), true) + TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1") != anno.end(), true) + TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-H3N1") != anno.end(), true) + TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-C1H2N2") != anno.end(), true) + TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-C1H2N1O1") != anno.end(), true) // test without prefix ion (but still requires correct losses elsewhere) tmp.clear(true); @@ -847,10 +847,10 @@ START_SECTION(([EXTRA] test first prefix loss)) TEST_EQUAL(tmp.size(), 99) // missing a1 and b1 ions as well as their losses -H3N1+ C1H2N2+ -C1H2N1O1+ anno = tmp.getStringDataArrays()[0]; - TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1+") == anno.end(), true) - TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-H3N1+") == anno.end(), true) - TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-C1H2N2+") == anno.end(), true) - TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-C1H2N1O1+") == anno.end(), true) + TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1") == anno.end(), true) + TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-H3N1") == anno.end(), true) + TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-C1H2N2") == anno.end(), true) + TEST_EQUAL(std::find(anno.begin(), anno.end(), "b1-C1H2N1O1") == anno.end(), true) } END_SECTION diff --git a/src/tests/topp/IDFileConverter_22_output.idXML b/src/tests/topp/IDFileConverter_22_output.idXML index 35ee1d14207..1b2ecc189fb 100644 --- a/src/tests/topp/IDFileConverter_22_output.idXML +++ b/src/tests/topp/IDFileConverter_22_output.idXML @@ -1,7 +1,7 @@ - + @@ -20,114 +20,114 @@ - + - + - + - + - + - - - - - - + + + + + + - + - - + + - + - - - - - + + + + + - - + + - - - - - - + + + + + + - + - - + + - + - - - - - + + + + + - + - - - - - + + + + + - + - - + + - + - - - - - + + + + + - - + + diff --git a/src/tests/topp/OpenNuXL_1_output.idXML b/src/tests/topp/OpenNuXL_1_output.idXML index cf72fd7df0c..91ccd8b1a4b 100644 --- a/src/tests/topp/OpenNuXL_1_output.idXML +++ b/src/tests/topp/OpenNuXL_1_output.idXML @@ -1,12 +1,12 @@ - + - + - + @@ -25,54 +25,72 @@ - - + + - + - - + + - - - - + + + + - - - - + + + + - + + + + + + + - - + + + + + + + + + - - + + + + + + + - + - + - + @@ -82,54 +100,72 @@ - - + + - + - - + + - - - - + + + + - - - - + + + + - + + + + + + + - - + + + + + + + + + - - + + + + + + + - + - + - + @@ -139,111 +175,147 @@ - - + + - + - - - + + + - - - - + + + + - - - - + + + + - + + + + + + + - + - - + + + + + + + + + - - + + + + + + + - - + + - - + + - + - - - - - - + + + + + + - - + + - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - + + + + + + + - - - + + + + + + + + + + - - + + + + + + + - - - + + + - + - + @@ -253,54 +325,72 @@ - - + + - + - - + + - - - - - + + + + + - - - - + + + + - + + + + + + + - - + + + + + + + + + - - + + + + + + + - - + + - + - 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- + @@ -1051,54 +1375,72 @@ - - + + - + - - - + + + - - - - - - - - + + + + + + + + - + + + + + + + - - + + + + + + + + + - - + + + + + + + - - - + + + - + - + @@ -1108,58 +1450,76 @@ - - + + - + - - - + + + - - - - - + + + + + - + - + - + + + + + + + - + + + + + + + + - - + + + + + + + - - - - - + + + + + - + - - - - - - + + + + + + diff --git a/src/tests/topp/OpenNuXL_2_output.idXML b/src/tests/topp/OpenNuXL_2_output.idXML index 057c2d857ce..01f01aeaf7d 100644 --- a/src/tests/topp/OpenNuXL_2_output.idXML +++ b/src/tests/topp/OpenNuXL_2_output.idXML @@ -1,12 +1,12 @@ - + - + - + @@ -14,636 +14,837 @@ - + + + + - + - + - - + + - + - - + + - - - - + + + + - - - - + + + + - + + + + + + + - - + + + + + + + + + - - + + + + + + + - + - + - + - + - - + + - + - - + + - - - - + + + + - - - - + + + + - + + + + + + + - - + + + + + + + + + - - + + + + + + + - + - + - + - + - - + + - + - - - + + + - - - - + + + + - - - - + + + + - + + + + + + + - + - - + + + + + + + + + - - + + + + + + + - - + + - 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306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 -17.788 712.7828 DECOY_Cas7 U-H2O1 KDDLNDAEAK 2 0.540192306041718 0.247234299778938 0 24.72 22.28 0 0 9.75 0 0 0 0 KdDLNDAEAK 1117.5251 306.0253 1423.5504 4.79 0.00 3.00 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 2 -18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 1.020841717720032 2.211100578308105 0 0 0 221.11 0 0 0 0 LDSkGNIK 873.4920 306.0253 1179.5173 23.87 0.00 8.44 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 -25.116 508.1855 Cas5 AU YTPYLGR 3 1.766234636306763 0.582297086715698 0 0 0 58.23 0 0 0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 3.66 1.70 0.00 0.44 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 -26.237 678.2844 Cas5 U DYHTVLGAR 2 10.246984481811523 0.669801533222199 0 5.20 66.98 0 38.44 0 0 0 0 DYhTVLGAR 1030.5196 324.0359 1354.5555 69.62 15.78 11.51 0.00 3.87 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 -26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 11.271114349365234 0.31447559595108 31.45 27.71 0 0 0 0 0 0 0 0 0 0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 -26.413 791.8590 DECOY_Cas7 U-H2O1 QDFREGLKQR 2 -4.288217067718506 0.0 0 0 0 0 0 0 0 0 0 0 QDFREGLKQR 1275.6684 306.0253 1581.6937 100.00 18.36 1.61 0.00 0.00 0.00 0.00 0.00 -0.0049 6.2 1582.7010 791.8541 528.2385 396.4307 2 -28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 7.450744152069092 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 -28.487 828.6961 DECOY_Cas5 CU-H2O1-H1O3P1 VAFQVSESLAQLSSTDDR 3 -4.445086002349854 1.08878767490387 108.88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 vAFQVSESLAQLSSTDDR 1951.9487 531.1003 2483.0490 51.11 11.72 1.86 0.00 1.35 0.00 0.00 0.00 -0.0058 7.0 2484.0562 1242.5318 828.6903 621.7695 2 -28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 3.044219493865967 0.0 0 0 0 0 0 0 0 0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 19.76 27.79 1.10 8.62 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 -31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 8.911904335021973 4.414139270782471 0 0 0 0 0 0 0 0 0 441.41 0 0 0 0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 -31.812 957.3968 DECOY_Cse2 U IQACSGNDLQQWAR 2 -0.950542509555817 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 IQACSGNDLQQWAR 1588.7416 324.0359 1912.7775 36.39 5.00 6.59 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 2 -33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.043148756027222 3.945903778076172 0 0 394.59 0 0 0 LLkVLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 -33.237 510.2805 DECOY_Cas7 U-H2O1 LVKLLK 2 -0.157985359430313 1.040942668914795 0 0 104.09 0 0 0 LVkLLK 712.5211 306.0253 1018.5464 14.44 0.97 1.30 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 -33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 4.868203163146973 0.0 0 0 0 0 0 0 0 0 0 0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 20.77 25.20 0.00 9.28 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 -34.016 790.8062 Cas7 U MATSGMMTELGK 2 11.939115524291992 3.298429727554321 329.84 0 0 0 0 0 0 0 0 0 0 0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 7.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 -34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 3.889295816421509 0.941199779510498 0 0 0 94.12 0 0 0 0 0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 17.30 22.18 0.00 31.68 0.00 0.00 2.21 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 -36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 9.927228927612305 2.236552476882935 0 0 0 0 0 0 223.66 0 0 0 0 0 0 0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 67.04 13.25 12.77 0.00 7.71 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 -36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 5.632431030273438 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 97.08 19.49 100.00 3.00 4.87 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 -37.098 735.8139 Cse1 U ALYTFAEGFK 2 11.312786102294922 1.498064517974854 16.33 0 0 88.31 118.17 130.54 0 149.81 138.77 0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 -37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 -2.599616527557373 0.0 0 0 0 0 0 0 0 0 0 0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 11.31 52.79 9.67 4.43 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 -37.536 833.8672 Cse2 U LVQPFGWENPR 2 3.501814842224121 4.441089153289795 0 0 0 0 0 0 444.11 0 0 0 0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 50.81 9.40 9.20 0.00 4.56 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 -37.864 698.2974 Cas5 U DEPMITLPR 2 6.724847316741943 0.301817148923874 0 0 30.18 0 0 0 0 17.27 0 DEpMITLPR 1070.5430 324.0359 1394.5789 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 -37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 -3.122588157653809 0.0 0 0 0 0 0 0 0 GNIKRCR 845.4654 549.1108 1394.5762 26.79 4.78 6.07 0.00 3.28 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 -39.118 623.2540 Cse2 U MLTWWGK 2 3.027589559555054 1.054794073104858 0 0 0 105.48 16.40 0 0 MLTwWGK 920.4578 324.0359 1244.4937 13.28 1.54 11.15 0.00 1.67 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 -39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 4.12628173828125 1.066928863525391 0 0 0 0 0 0 0 0 106.69 0 0 0 0 0 0 0 0 0 0 0 0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 -39.853 861.3889 DECOY_Cas5 U GTPRTGEFTPQGWAQMPGALR 3 0.42877921462059 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 GTPRTGEFTPQGWAQMPGALR 2257.1062 324.0359 2581.1421 18.90 4.27 4.11 0.00 2.47 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 2 -40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 -1.674614667892456 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 12.49 1.88 1.47 0.00 0.00 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 +17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 11.758779525756836 5.191475868225098 0,0,102.69,0,0,54.62,0,0,0,519.15 AEADNLDDKk 1117.5251 306.0253 1423.5504 21.88 0.00 17.32 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 +17.788 712.7828 DECOY_Cas7 U-H2O1 DDLNDAEAKK 2 0.856053352355957 0.89695680141449 0,0,0,0,0,0,0,0,0,89.70 DDLNDAEAKk 1117.5251 306.0253 1423.5504 21.88 0.00 17.32 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 2 +18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 3.949868440628052 3.232806921005249 0,0,0,323.28,0,0,0,0 LDSkGNIK 873.4920 306.0253 1179.5173 48.85 0.00 29.05 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 +18.306 590.7661 DECOY_Cas6e U-H2O1 SDLKINGK 2 2.111494541168213 0.0 0,0,0,0,0,0,0,0 SDLKINGK 873.4920 306.0253 1179.5173 48.85 0.00 29.05 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 2 +25.116 508.1855 Cas5 AU YTPYLGR 3 4.332501411437988 2.260403633117676 0,0,0,226.04,0,0,0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 19.14 9.59 0.00 6.66 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 +26.237 678.2844 Cas5 U DYHTVLGAR 2 14.116133689880371 1.70267391204834 0,22.80,0,0,170.27,0,0,0,0 DYHTvLGAR 1030.5196 324.0359 1354.5555 83.44 39.73 33.92 0.00 19.68 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 +26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 20.954658508300781 1.743481516838074 174.35,147.04,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 42.85 12.68 0.00 6.24 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 +26.413 791.8590 DECOY_Cse2 U-H2O1 KGLSIGTTQESR 2 1.59760046005249 0.0 0,0,0,0,0,0,0,0,0,0,0,0 KGLSIGTTQESR 1275.6783 306.0253 1581.7036 100.00 42.85 12.68 0.00 6.24 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 2 +28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 14.908589363098145 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 71.49 34.24 0.00 0.00 11.61 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 +28.487 828.6961 DECOY_Cas6e U ESIPHVDEVRGDGSFYQPK 3 2.75232458114624 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 ESIPHVDEVRGDGSFYQPK 2159.0284 324.0359 2483.0642 71.49 34.24 0.00 0.00 11.61 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 2 +28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 4.606048583984375 0.0 0,0,0,0,0,0,0,0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 44.45 52.71 10.50 29.37 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 +31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 14.243102073669434 12.029438972473145 0,0,0,0,0,0,0,0,0,1202.94,0,0,0,0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 63.71 23.62 27.11 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 +31.812 957.3968 DECOY_Cse2 GU-H2O1-H1O3P1 PNEWGFPQVLR 2 2.444492101669312 0.0 0,0,0,0,0,0,0,0,0,0,0 PNEWGFPQVLR 1341.6830 571.1064 1912.7894 63.71 23.62 27.11 0.00 0.00 0.00 0.00 0.00 0.0052 -5.4 1913.7967 957.4020 638.6037 479.2046 2 +33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.928004741668701 6.037654399871826 0,0,603.77,0,0,0 LLkVLK 712.5211 306.0253 1018.5464 38.00 9.85 11.39 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 +33.237 510.2805 DECOY_Cas7 U-H2O1 LLKLVK 2 2.917794466018677 5.519994258880615 0,0,552.00,0,0,0 LLkLVK 712.5211 306.0253 1018.5464 38.00 9.85 11.39 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 +33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 10.801374435424805 0.0 0,0,0,0,0,0,0,0,0,0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 45.57 50.20 0.00 30.46 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 +33.791 717.3553 DECOY_Cas7 U-H2O1 LVKIAAIDER 2 2.084635972976685 0.0 0,0,0,0,0,0,0,0,0,0 LVKIAAIDER 1126.6710 306.0253 1432.6963 100.00 45.57 50.20 0.00 30.46 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 2 +34.016 790.8062 Cas7 U MATSGMMTELGK 2 21.774337768554688 6.851785659790039 685.18,0,0,0,0,0,0,0,0,0,0,0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 27.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 +34.016 790.8062 DECOY_Cas7 U GLETMMGSTAMK 2 1.707732081413269 0.0 0,0,0,0,0,0,0,0,0,0,0,0 GLETMMGSTAMK 1255.5611 324.0359 1579.5969 27.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 2 +34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 6.025181770324707 3.57084846496582 0,0,0,357.08,0,0,0,0,0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 41.59 47.10 0.00 56.28 0.00 0.00 14.85 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 +36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 14.701607704162598 5.398694038391113 0,0,0,0,0,0,539.87,0,0,0,0,0,0,0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 81.88 36.40 35.73 0.00 27.77 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 +36.528 938.3693 DECOY_Cas7 U-H2O1 QMNMDDKGGFIADK 2 2.078341245651245 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0 QMNMDDKGGFIADK 1568.6963 306.0253 1874.7216 81.88 36.40 35.73 0.00 27.77 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 2 +36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 11.384106636047363 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 98.53 44.15 100.00 17.32 22.07 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 +36.767 933.9406 DECOY_Cas7 U-H2O1 GSLLALTKEAEDVSK 2 1.830352663993836 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 GSLLALTKEAEDVSK 1559.8407 306.0253 1865.8660 98.53 44.15 100.00 17.32 22.07 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 2 +37.098 735.8139 Cse1 U ALYTFAEGFK 2 17.351419448852539 4.97014331817627 53.13,0,0,0,387.97,413.74,0,497.01,473.80,0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 33.63 72.66 31.10 21.04 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 +37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 0.900696098804474 0.0 0,0,0,0,0,0,0,0,0,0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 33.63 72.66 31.10 21.04 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 +37.536 833.8672 Cse2 U LVQPFGWENPR 2 6.86949348449707 9.78563404083252 0,0,0,0,0,0,978.56,0,0,0,0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 71.28 30.66 30.33 0.00 21.35 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 +37.536 833.8672 DECOY_Cse2 U PNEWGFPQVLR 2 1.99531888961792 0.728722631931305 0,0,0,72.87,0,0,0,0,0,0,0 PNEwGFPQVLR 1341.6830 324.0359 1665.7188 71.28 30.66 30.33 0.00 21.35 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 2 +37.864 698.2974 Cas5 U DEPMITLPR 2 9.813562393188477 1.514074325561523 0,0,151.41,0,0,0,0,44.15,0 DEpMITLPR 1070.5430 324.0359 1394.5789 51.76 21.86 24.64 0.00 18.10 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 +37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 1.017842531204224 0.0 0,0,0,0,0,0,0 GNIKRCR 845.4654 549.1108 1394.5762 51.76 21.86 24.64 0.00 18.10 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 +39.118 623.2540 Cse2 U MLTWWGK 2 4.790749549865723 3.865850687026978 0,0,0,386.59,62.76,0,0 MLTwWGK 920.4578 324.0359 1244.4937 36.44 12.42 33.38 0.00 12.90 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 +39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 11.862678527832031 6.160688877105713 0,0,0,0,0,0,0,0,616.07,0,0,0,0,0,0,0,0,0,0,0,0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 43.47 20.67 20.27 0.00 15.70 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 +39.853 861.3889 DECOY_Cas5 U TGEFTPQGWAQMPGALRGTPR 3 2.125545740127563 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 TGEFTPQGWAQMPGALRGTPR 2257.1062 324.0359 2581.1421 43.47 20.67 20.27 0.00 15.70 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 2 +40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 5.287387371063232 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 35.35 13.70 12.12 0.00 9.76 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 diff --git a/src/tests/topp/OpenNuXL_5_output.idXML b/src/tests/topp/OpenNuXL_5_output.idXML index 6c859e2674f..bc5dc2f9c2c 100644 --- a/src/tests/topp/OpenNuXL_5_output.idXML +++ b/src/tests/topp/OpenNuXL_5_output.idXML @@ -1,12 +1,12 @@ - + - + - + @@ -25,625 +25,823 @@ - - + + - + - - + + - - - - + + + + - - - - - 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b/src/tests/topp/SimpleSearchEngine_1_out.idXML index 0a4ba8f40b1..5e094640f1f 100644 --- a/src/tests/topp/SimpleSearchEngine_1_out.idXML +++ b/src/tests/topp/SimpleSearchEngine_1_out.idXML @@ -1,10 +1,10 @@ - + - + @@ -19,14 +19,14 @@ - + - + diff --git a/src/topp/IDFileConverter.cpp b/src/topp/IDFileConverter.cpp index 3efc90334e5..76e1310ee23 100644 --- a/src/topp/IDFileConverter.cpp +++ b/src/topp/IDFileConverter.cpp @@ -182,9 +182,6 @@ class TOPPIDFileConverter : FileHandler().loadExperiment(filename, expmap); lookup.readSpectra(expmap.getSpectra()); -#ifdef _OPENMP -#pragma omp parallel for -#endif for (SignedSize i = 0; i < (SignedSize)peptide_identifications.size(); ++i) { try @@ -195,9 +192,6 @@ class TOPPIDFileConverter : } catch (Exception::ElementNotFound&) { -#ifdef _OPENMP -#pragma omp critical (IDFileConverter_ERROR) -#endif { OPENMS_LOG_ERROR << "Error: Failed to look up spectrum - none with corresponding native ID found." << endl; ret = false; diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 8291891c133..1c8d712b06e 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -3856,7 +3856,7 @@ static void scoreXLIons_( p.setValue("precursor:isotopes", IntList{0, 1}); p.setValue("decoys", generate_decoys ? "true" : "false"); p.setValue("enzyme", getStringOption_("peptide:enzyme")); - p.setValue("annotate:PSM", StringList{"median_fragment_error_ppm", "precursor_error_ppm"}); + p.setValue("annotate:PSM", StringList{Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM, Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM}); sse.setParameters(p); cout << "Running autotune..." << endl; sse.search(in_mzml, in_db, prot_ids, pep_ids); @@ -3935,14 +3935,14 @@ static void scoreXLIons_( for (const auto& pi : pep_ids) { const PeptideHit& ph = pi.getHits()[0]; - if (ph.metaValueExists("median_fragment_error_ppm")) + if (ph.metaValueExists(Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM)) { //cout << ph.getMetaValue("median_fragment_error_ppm") << endl; - median_fragment_error_ppm.push_back(fabs((double)ph.getMetaValue("median_fragment_error_ppm"))); + median_fragment_error_ppm.push_back(fabs((double)ph.getMetaValue(Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM))); } - if (ph.metaValueExists("precursor_error_ppm")) + if (ph.metaValueExists(Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM)) { - precursor_error_ppm.push_back((double)ph.getMetaValue("precursor_error_ppm")); + precursor_error_ppm.push_back((double)ph.getMetaValue(Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM)); } } sort(median_fragment_error_ppm.begin(), median_fragment_error_ppm.end()); From 6d6083fe95daf77483aaf3f414fec642ef8f6813 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 5 May 2020 23:46:29 +0200 Subject: [PATCH 108/471] REVERT additional check in deisotoper because of failing SwathQC test --- .../FILTERING/DATAREDUCTION/Deisotoper.cpp | 3 +- src/tests/topp/OpenNuXL_1_output.idXML | 418 +++++----- src/tests/topp/OpenNuXL_2_output.idXML | 418 +++++----- src/tests/topp/OpenNuXL_3_output.idXML | 494 ++++++------ src/tests/topp/OpenNuXL_4_output.idXML | 740 +++++++++--------- src/tests/topp/OpenNuXL_4_output2.tsv | 46 +- src/tests/topp/OpenNuXL_5_output.idXML | 530 ++++++------- src/tests/topp/SimpleSearchEngine_1_out.idXML | 6 +- 8 files changed, 1328 insertions(+), 1327 deletions(-) diff --git a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp index cbae924e215..dd76647ff6b 100644 --- a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp +++ b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp @@ -163,13 +163,14 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, break; } +/* // ratio of first isotopic peak to monoisotopic peak may not be too large if (i == 1 && old_spectrum[p].getIntensity() / old_spectrum[extensions.back()].getIntensity() > 10.0) { has_min_isopeaks = (i >= min_isopeaks); break; } - +*/ // averagine check passed or skipped extensions.push_back(p); if (annotate_iso_peak_count) diff --git a/src/tests/topp/OpenNuXL_1_output.idXML b/src/tests/topp/OpenNuXL_1_output.idXML index 91ccd8b1a4b..098b348aec2 100644 --- a/src/tests/topp/OpenNuXL_1_output.idXML +++ b/src/tests/topp/OpenNuXL_1_output.idXML @@ -6,7 +6,7 @@ - + @@ -100,10 +100,10 @@ - - + + - + @@ -111,30 +111,30 @@ - + - + - + - + - + - + - - + + @@ -144,8 +144,8 @@ - - + + @@ -175,52 +175,52 @@ - - + + - + - - + + - + - - - - + + + + - - + + - + - - + + - + - - + + @@ -325,33 +325,33 @@ - + - + - + - + - + - + - + - + - + @@ -362,15 +362,15 @@ - + - - + + @@ -400,33 +400,33 @@ - - + + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -437,15 +437,15 @@ - + - - + + @@ -550,52 +550,52 @@ - - + + - + - + - - - - - - - - - + + + + + + + + + - - + + - + - - + + - + - - + + @@ -625,33 +625,33 @@ - - + + - + - + - - - + + + - + - + - - + + - + @@ -662,15 +662,15 @@ - + - - + + @@ -775,10 +775,10 @@ - - + + - + @@ -786,41 +786,41 @@ - + - + - - - - + + + + - + - + - - + + - + - - + + @@ -925,33 +925,33 @@ - - + + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -962,15 +962,15 @@ - + - - + + @@ -1075,33 +1075,33 @@ - - + + - + - - - + + + - + - + - + - + - + - + @@ -1112,15 +1112,15 @@ - + - - + + @@ -1150,33 +1150,33 @@ - - + + - + - - + + - - - - - + + + + + - + - - + + - + @@ -1187,15 +1187,15 @@ - + - - + + @@ -1225,33 +1225,33 @@ - - + + - + - - + + - + - + - + - + - + - + @@ -1262,15 +1262,15 @@ - + - - + + @@ -1300,41 +1300,41 @@ - - + + - + - + - - + + - + - - - - + + + + - - + + - + - - + + @@ -1344,8 +1344,8 @@ - - + + @@ -1450,33 +1450,33 @@ - + - + - + - + - + - + - + - + - + - + @@ -1487,15 +1487,15 @@ - + - - + + diff --git a/src/tests/topp/OpenNuXL_2_output.idXML b/src/tests/topp/OpenNuXL_2_output.idXML index 01f01aeaf7d..3b448cd9fb9 100644 --- a/src/tests/topp/OpenNuXL_2_output.idXML +++ b/src/tests/topp/OpenNuXL_2_output.idXML @@ -6,7 +6,7 @@ - + @@ -105,9 +105,9 @@ - + - + @@ -115,30 +115,30 @@ - + - + - + - + - + - + - - + + @@ -148,8 +148,8 @@ - - + + @@ -174,58 +174,58 @@ - + - + - + - - + + - + - - - - + + + + - - + + - + - - + + - + - - + + @@ -250,7 +250,7 @@ - + @@ -335,30 +335,30 @@ - + - + - + - + - + - + - + - + @@ -369,15 +369,15 @@ - + - - + + @@ -402,39 +402,39 @@ - + - + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -445,15 +445,15 @@ - + - - + + @@ -478,7 +478,7 @@ - + @@ -561,51 +561,51 @@ - + - + - + - - - - - - - - - + + + + + + + + + - - + + - + - - + + - + - - + + @@ -630,39 +630,39 @@ - + - + - + - + - - - + + + - + - + - - + + - + @@ -673,15 +673,15 @@ - + - - + + @@ -706,7 +706,7 @@ - + @@ -789,9 +789,9 @@ - + - + @@ -799,41 +799,41 @@ - + - + - - - - + + + + - + - + - - + + - + - - + + @@ -858,7 +858,7 @@ - + @@ -941,32 +941,32 @@ - + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -977,15 +977,15 @@ - + - - + + @@ -1010,7 +1010,7 @@ - + @@ -1093,32 +1093,32 @@ - + - + - - - + + + - + - + - + - + - + - + @@ -1129,15 +1129,15 @@ - + - - + + @@ -1162,39 +1162,39 @@ - + - + - + - - + + - - - - - + + + + + - + - - + + - + @@ -1205,15 +1205,15 @@ - + - - + + @@ -1238,39 +1238,39 @@ - + - + - + - - + + - + - + - + - + - + - + @@ -1281,15 +1281,15 @@ - + - - + + @@ -1314,47 +1314,47 @@ - + - + - + - + - - + + - + - - - - + + + + - - + + - + - - + + @@ -1364,8 +1364,8 @@ - - + + @@ -1390,7 +1390,7 @@ - + @@ -1475,30 +1475,30 @@ - + - + - + - + - + - + - + - + - + @@ -1509,15 +1509,15 @@ - + - - + + @@ -1542,7 +1542,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_3_output.idXML b/src/tests/topp/OpenNuXL_3_output.idXML index 55dfb5bdca5..7baba2038f9 100644 --- a/src/tests/topp/OpenNuXL_3_output.idXML +++ b/src/tests/topp/OpenNuXL_3_output.idXML @@ -6,7 +6,7 @@ - + @@ -100,10 +100,10 @@ - - + + - + @@ -111,30 +111,30 @@ - + - + - + - + - + - + - - + + @@ -144,8 +144,8 @@ - - + + @@ -175,52 +175,52 @@ - - + + - + - - + + - + - - - - + + + + - - + + - + - - + + - + - - + + @@ -325,33 +325,33 @@ - + - + - + - + - + - + - + - + - + @@ -362,15 +362,15 @@ - + - - + + @@ -396,33 +396,33 @@ - + - + - + - + - + - + - + - + - + - + @@ -433,15 +433,15 @@ - + - - + + @@ -467,33 +467,33 @@ - - + + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -504,15 +504,15 @@ - + - - + + @@ -538,33 +538,33 @@ - - + + - + - + - + - + - + - + - + - + @@ -575,15 +575,15 @@ - + - - + + @@ -684,52 +684,52 @@ - - + + - + - + - - - - - - - - - + + + + + + + + + - - + + - + - - + + - + - - + + @@ -759,33 +759,33 @@ - - + + - + - + - - - + + + - + - + - - + + - + @@ -796,15 +796,15 @@ - + - - + + @@ -909,10 +909,10 @@ - - + + - + @@ -920,41 +920,41 @@ - + - + - - - - + + + + - + - + - - + + - + - - + + @@ -1059,33 +1059,33 @@ - - + + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -1096,15 +1096,15 @@ - + - - + + @@ -1209,33 +1209,33 @@ - - + + - + - - - + + + - + - + - + - + - + - + @@ -1246,15 +1246,15 @@ - + - - + + @@ -1284,33 +1284,33 @@ - - + + - + - - + + - - - - - + + + + + - + - - + + - + @@ -1321,15 +1321,15 @@ - + - - + + @@ -1359,33 +1359,33 @@ - - + + - + - - + + - + - + - + - + - + - + @@ -1396,15 +1396,15 @@ - + - - + + @@ -1430,33 +1430,33 @@ - + - + - + - + - + - + - + - + - + @@ -1467,15 +1467,15 @@ - + - - + + @@ -1501,41 +1501,41 @@ - - + + - + - + - - + + - + - - - - + + + + - - + + - + - - + + @@ -1545,8 +1545,8 @@ - - + + @@ -1651,33 +1651,33 @@ - + - + - + - + - + - + - + - + - + - + @@ -1688,15 +1688,15 @@ - + - - + + diff --git a/src/tests/topp/OpenNuXL_4_output.idXML b/src/tests/topp/OpenNuXL_4_output.idXML index ed0c58892f2..fe17870de8a 100644 --- a/src/tests/topp/OpenNuXL_4_output.idXML +++ b/src/tests/topp/OpenNuXL_4_output.idXML @@ -6,7 +6,7 @@ - + @@ -185,9 +185,9 @@ - + - + @@ -195,30 +195,30 @@ - + - + - + - + - + - + - - + + @@ -228,8 +228,8 @@ - - + + @@ -254,12 +254,12 @@ - + - + @@ -267,22 +267,22 @@ - + - + - + - + - + - + @@ -300,8 +300,8 @@ - - + + @@ -322,58 +322,58 @@ - + - + - + - - + + - + - - - - + + + + - - + + - + - - + + - + - - + + @@ -398,7 +398,7 @@ - + @@ -483,30 +483,30 @@ - + - + - + - + - + - + - + - + @@ -517,15 +517,15 @@ - + - - + + @@ -550,35 +550,35 @@ - + - + - + - + - + - + - + - + - + @@ -589,15 +589,15 @@ - + - - + + @@ -618,39 +618,39 @@ - + - + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -661,15 +661,15 @@ - + - - + + @@ -694,35 +694,35 @@ - + - + - + - - + + - - - - - - - - - + + + + + + + + + - - + + - + @@ -733,15 +733,15 @@ - + - - + + @@ -762,7 +762,7 @@ - + @@ -845,51 +845,51 @@ - + - + - + - - - - - - - - - + + + + + + + + + - - + + - + - - + + - + - - + + @@ -914,60 +914,60 @@ - + - - + + - + - - + + - - - - - - - - + + + + + + + + - - + + - - - + + + - + - - + + - + - - - + + + - - + + @@ -976,45 +976,45 @@ - - - - - - - + + + + + + + - + - + - + - - - + + + - + - + - - + + - + @@ -1025,15 +1025,15 @@ - + - - + + @@ -1058,35 +1058,35 @@ - + - + - + - + - - - + + + - + - + - - + + - + @@ -1097,15 +1097,15 @@ - + - - + + @@ -1126,7 +1126,7 @@ - + @@ -1277,9 +1277,9 @@ - + - + @@ -1287,41 +1287,41 @@ - + - + - - - - + + + + - + - + - - + + - + - - + + @@ -1346,12 +1346,12 @@ - + - + - + @@ -1359,22 +1359,22 @@ - + - + - + - + - + - + @@ -1385,15 +1385,15 @@ - + - - + + @@ -1414,7 +1414,7 @@ - + @@ -1497,32 +1497,32 @@ - + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -1533,15 +1533,15 @@ - + - - + + @@ -1566,35 +1566,35 @@ - + - - + + - + - - + + - + - - - - - + + + + + - + - - + + - + @@ -1605,15 +1605,15 @@ - + - - + + @@ -1634,7 +1634,7 @@ - + @@ -1785,32 +1785,32 @@ - + - + - - - + + + - + - + - + - + - + - + @@ -1821,15 +1821,15 @@ - + - - + + @@ -1854,35 +1854,35 @@ - + - + - + - - - + + + - + - + - + - + - + - + @@ -1893,15 +1893,15 @@ - + - - + + @@ -1922,39 +1922,39 @@ - + - + - + - - + + - - - - - + + + + + - + - - + + - + @@ -1965,15 +1965,15 @@ - + - - + + @@ -1998,35 +1998,35 @@ - + - + - + - + - + - + - + - + - + @@ -2037,15 +2037,15 @@ - + - - + + @@ -2066,39 +2066,39 @@ - + - + - + - - + + - + - + - + - + - + - + @@ -2109,15 +2109,15 @@ - + - - + + @@ -2142,35 +2142,35 @@ - + - + - + - + - + - + - + - + - + @@ -2181,15 +2181,15 @@ - + - - + + @@ -2210,47 +2210,47 @@ - + - + - + - + - - + + - + - - - - + + + + - - + + - + - - + + @@ -2260,8 +2260,8 @@ - - + + @@ -2286,7 +2286,7 @@ - + @@ -2439,30 +2439,30 @@ - + - + - + - + - + - + - + - + - + @@ -2473,15 +2473,15 @@ - + - - + + @@ -2506,7 +2506,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_4_output2.tsv b/src/tests/topp/OpenNuXL_4_output2.tsv index a632615bded..4433d9b7491 100644 --- a/src/tests/topp/OpenNuXL_4_output2.tsv +++ b/src/tests/topp/OpenNuXL_4_output2.tsv @@ -1,35 +1,35 @@ #RT original m/z proteins RNA peptide charge score best localization score localization scores best localization(s) peptide weight RNA weight cross-link weight A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H rank 17.788 712.7828 Cas7 U-H2O1 AEADNLDDKK 2 11.758779525756836 5.191475868225098 0,0,102.69,0,0,54.62,0,0,0,519.15 AEADNLDDKk 1117.5251 306.0253 1423.5504 21.88 0.00 17.32 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 1 17.788 712.7828 DECOY_Cas7 U-H2O1 DDLNDAEAKK 2 0.856053352355957 0.89695680141449 0,0,0,0,0,0,0,0,0,89.70 DDLNDAEAKk 1117.5251 306.0253 1423.5504 21.88 0.00 17.32 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 2 -18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 3.949868440628052 3.232806921005249 0,0,0,323.28,0,0,0,0 LDSkGNIK 873.4920 306.0253 1179.5173 48.85 0.00 29.05 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 -18.306 590.7661 DECOY_Cas6e U-H2O1 SDLKINGK 2 2.111494541168213 0.0 0,0,0,0,0,0,0,0 SDLKINGK 873.4920 306.0253 1179.5173 48.85 0.00 29.05 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 2 -25.116 508.1855 Cas5 AU YTPYLGR 3 4.332501411437988 2.260403633117676 0,0,0,226.04,0,0,0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 19.14 9.59 0.00 6.66 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 +18.306 590.7661 Cas6e U-H2O1 LDSKGNIK 2 3.952725648880005 2.508852005004883 0,0,0,250.89,0,0,0,0 LDSkGNIK 873.4920 306.0253 1179.5173 48.85 0.00 29.05 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 1 +18.306 590.7661 DECOY_Cas6e U-H2O1 SDLKINGK 2 2.112793207168579 0.0 0,0,0,0,0,0,0,0 SDLKINGK 873.4920 306.0253 1179.5173 48.85 0.00 29.05 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 2 +25.116 508.1855 Cas5 AU YTPYLGR 3 4.319485664367676 2.036591768264771 0,0,0,203.66,0,0,0 YTPyLGR 868.4443 653.0884 1521.5327 100.00 19.14 9.59 0.00 6.66 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 1 26.237 678.2844 Cas5 U DYHTVLGAR 2 14.116133689880371 1.70267391204834 0,22.80,0,0,170.27,0,0,0,0 DYHTvLGAR 1030.5196 324.0359 1354.5555 83.44 39.73 33.92 0.00 19.68 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 1 -26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 20.954658508300781 1.743481516838074 174.35,147.04,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 42.85 12.68 0.00 6.24 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 -26.413 791.8590 DECOY_Cse2 U-H2O1 KGLSIGTTQESR 2 1.59760046005249 0.0 0,0,0,0,0,0,0,0,0,0,0,0 KGLSIGTTQESR 1275.6783 306.0253 1581.7036 100.00 42.85 12.68 0.00 6.24 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 2 -28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 14.908589363098145 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 71.49 34.24 0.00 0.00 11.61 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 -28.487 828.6961 DECOY_Cas6e U ESIPHVDEVRGDGSFYQPK 3 2.75232458114624 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 ESIPHVDEVRGDGSFYQPK 2159.0284 324.0359 2483.0642 71.49 34.24 0.00 0.00 11.61 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 2 +26.413 791.8590 Cse2 U-H2O1 KSEQTTGISLGR 2 20.955133438110352 1.743481516838074 174.35,147.04,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 100.00 42.85 12.68 0.00 6.24 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 1 +26.413 791.8590 DECOY_Cse2 U-H2O1 KGLSIGTTQESR 2 1.597686409950256 0.0 0,0,0,0,0,0,0,0,0,0,0,0 KGLSIGTTQESR 1275.6783 306.0253 1581.7036 100.00 42.85 12.68 0.00 6.24 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 2 +28.487 828.6961 Cas6e U VEDVHPISERPQYFSGDGK 3 13.217598915100098 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 71.49 34.24 0.00 0.00 11.61 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 1 +28.487 828.6961 DECOY_Cas6e U ESIPHVDEVRGDGSFYQPK 3 2.377058267593384 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 ESIPHVDEVRGDGSFYQPK 2159.0284 324.0359 2483.0642 71.49 34.24 0.00 0.00 11.61 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 2 28.678 656.7949 Cas7 U-H2O1 FDQKIIDK 2 4.606048583984375 0.0 0,0,0,0,0,0,0,0 FDQKIIDK 1005.5495 306.0253 1311.5748 100.00 44.45 52.71 10.50 29.37 0.00 0.00 0.00 -0.0002 0.4 1312.5821 656.7947 438.1989 328.9010 1 -31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 14.243102073669434 12.029438972473145 0,0,0,0,0,0,0,0,0,1202.94,0,0,0,0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 63.71 23.62 27.11 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 -31.812 957.3968 DECOY_Cse2 GU-H2O1-H1O3P1 PNEWGFPQVLR 2 2.444492101669312 0.0 0,0,0,0,0,0,0,0,0,0,0 PNEWGFPQVLR 1341.6830 571.1064 1912.7894 63.71 23.62 27.11 0.00 0.00 0.00 0.00 0.00 0.0052 -5.4 1913.7967 957.4020 638.6037 479.2046 2 -33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.928004741668701 6.037654399871826 0,0,603.77,0,0,0 LLkVLK 712.5211 306.0253 1018.5464 38.00 9.85 11.39 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 -33.237 510.2805 DECOY_Cas7 U-H2O1 LLKLVK 2 2.917794466018677 5.519994258880615 0,0,552.00,0,0,0 LLkLVK 712.5211 306.0253 1018.5464 38.00 9.85 11.39 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 +31.812 957.3968 Cse2 U AWQQLDNGSCAQIR 2 10.819504737854004 11.234766960144043 0,0,0,0,0,0,0,0,0,1123.48,0,0,0,0 AWQQLDNGScAQIR 1588.7416 324.0359 1912.7775 63.71 23.62 27.11 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 1 +31.812 957.3968 DECOY_Cse2 U IQACSGNDLQQWAR 2 1.573387980461121 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0 IQACSGNDLQQWAR 1588.7416 324.0359 1912.7775 63.71 23.62 27.11 0.00 0.00 0.00 0.00 0.00 -0.0008 0.8 1913.7848 957.3960 638.5998 479.2017 2 +33.237 510.2805 Cas7 U-H2O1 LLKVLK 2 2.729134798049927 6.037654399871826 0,0,603.77,0,0,0 LLkVLK 712.5211 306.0253 1018.5464 38.00 9.85 11.39 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 1 +33.237 510.2805 DECOY_Cas7 U-H2O1 LLKLVK 2 2.718602895736694 5.519994258880615 0,0,552.00,0,0,0 LLkLVK 712.5211 306.0253 1018.5464 38.00 9.85 11.39 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 2 33.791 717.3553 Cas7 U-H2O1 VLKEDIAAIR 2 10.801374435424805 0.0 0,0,0,0,0,0,0,0,0,0 VLKEDIAAIR 1126.6710 306.0253 1432.6963 100.00 45.57 50.20 0.00 30.46 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 1 33.791 717.3553 DECOY_Cas7 U-H2O1 LVKIAAIDER 2 2.084635972976685 0.0 0,0,0,0,0,0,0,0,0,0 LVKIAAIDER 1126.6710 306.0253 1432.6963 100.00 45.57 50.20 0.00 30.46 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 2 -34.016 790.8062 Cas7 U MATSGMMTELGK 2 21.774337768554688 6.851785659790039 685.18,0,0,0,0,0,0,0,0,0,0,0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 27.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 -34.016 790.8062 DECOY_Cas7 U GLETMMGSTAMK 2 1.707732081413269 0.0 0,0,0,0,0,0,0,0,0,0,0,0 GLETMMGSTAMK 1255.5611 324.0359 1579.5969 27.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 2 +34.016 790.8062 Cas7 U MATSGMMTELGK 2 21.774127960205078 6.40651798248291 640.65,0,0,0,0,0,0,0,0,0,0,0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 27.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 1 +34.016 790.8062 DECOY_Cas7 U GLETMMGSTAMK 2 1.707939863204956 0.0 0,0,0,0,0,0,0,0,0,0,0,0 GLETMMGSTAMK 1255.5611 324.0359 1579.5969 27.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 2 34.072 648.2559 Cse2 U M(Oxidation)VFCLSAGK 2 6.025181770324707 3.57084846496582 0,0,0,357.08,0,0,0,0,0 MVFcLSAGK 970.4616 324.0359 1294.4975 100.00 41.59 47.10 0.00 56.28 0.00 0.00 14.85 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 1 -36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 14.701607704162598 5.398694038391113 0,0,0,0,0,0,539.87,0,0,0,0,0,0,0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 81.88 36.40 35.73 0.00 27.77 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 -36.528 938.3693 DECOY_Cas7 U-H2O1 QMNMDDKGGFIADK 2 2.078341245651245 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0 QMNMDDKGGFIADK 1568.6963 306.0253 1874.7216 81.88 36.40 35.73 0.00 27.77 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 2 +36.528 938.3693 Cas7 U-H2O1 DDMNMQKDAIFGGK 2 12.813339233398438 5.398694038391113 0,0,0,0,0,0,539.87,0,0,0,0,0,0,0 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 81.88 36.40 35.73 0.00 27.77 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 1 +36.528 938.3693 DECOY_Cas7 U-H2O1 QMNMDDKGGFIADK 2 1.047281980514526 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0 QMNMDDKGGFIADK 1568.6963 306.0253 1874.7216 81.88 36.40 35.73 0.00 27.77 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 2 36.767 933.9406 Cas7 U-H2O1 TLALLSGKSVDEAEK 2 11.384106636047363 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 TLALLSGKSVDEAEK 1559.8407 306.0253 1865.8660 98.53 44.15 100.00 17.32 22.07 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 1 36.767 933.9406 DECOY_Cas7 U-H2O1 GSLLALTKEAEDVSK 2 1.830352663993836 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 GSLLALTKEAEDVSK 1559.8407 306.0253 1865.8660 98.53 44.15 100.00 17.32 22.07 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 2 -37.098 735.8139 Cse1 U ALYTFAEGFK 2 17.351419448852539 4.97014331817627 53.13,0,0,0,387.97,413.74,0,497.01,473.80,0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 33.63 72.66 31.10 21.04 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 -37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 0.900696098804474 0.0 0,0,0,0,0,0,0,0,0,0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 33.63 72.66 31.10 21.04 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 -37.536 833.8672 Cse2 U LVQPFGWENPR 2 6.86949348449707 9.78563404083252 0,0,0,0,0,0,978.56,0,0,0,0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 71.28 30.66 30.33 0.00 21.35 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 -37.536 833.8672 DECOY_Cse2 U PNEWGFPQVLR 2 1.99531888961792 0.728722631931305 0,0,0,72.87,0,0,0,0,0,0,0 PNEwGFPQVLR 1341.6830 324.0359 1665.7188 71.28 30.66 30.33 0.00 21.35 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 2 -37.864 698.2974 Cas5 U DEPMITLPR 2 9.813562393188477 1.514074325561523 0,0,151.41,0,0,0,0,44.15,0 DEpMITLPR 1070.5430 324.0359 1394.5789 51.76 21.86 24.64 0.00 18.10 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 -37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 1.017842531204224 0.0 0,0,0,0,0,0,0 GNIKRCR 845.4654 549.1108 1394.5762 51.76 21.86 24.64 0.00 18.10 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 -39.118 623.2540 Cse2 U MLTWWGK 2 4.790749549865723 3.865850687026978 0,0,0,386.59,62.76,0,0 MLTwWGK 920.4578 324.0359 1244.4937 36.44 12.42 33.38 0.00 12.90 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 +37.098 735.8139 Cse1 U ALYTFAEGFK 2 17.346786499023438 4.97014331817627 53.13,0,0,0,387.97,413.74,0,497.01,473.80,0 ALYTFAEgFK 1145.5757 324.0359 1469.6116 100.00 33.63 72.66 31.10 21.04 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 1 +37.098 735.8139 DECOY_Cse1 U FGEAFTYLAK 2 0.893929243087769 0.0 0,0,0,0,0,0,0,0,0,0 FGEAFTYLAK 1145.5757 324.0359 1469.6116 100.00 33.63 72.66 31.10 21.04 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 2 +37.536 833.8672 Cse2 U LVQPFGWENPR 2 5.253974914550781 9.78563404083252 0,0,0,0,0,0,978.56,0,0,0,0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 71.28 30.66 30.33 0.00 21.35 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 1 +37.536 833.8672 DECOY_Cse2 U PNEWGFPQVLR 2 1.995638847351074 0.728722631931305 0,0,0,72.87,0,0,0,0,0,0,0 PNEwGFPQVLR 1341.6830 324.0359 1665.7188 71.28 30.66 30.33 0.00 21.35 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 2 +37.864 698.2974 Cas5 U DEPMITLPR 2 9.814291954040527 1.514074325561523 0,0,151.41,0,0,0,0,44.15,0 DEpMITLPR 1070.5430 324.0359 1394.5789 51.76 21.86 24.64 0.00 18.10 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 1 +37.864 698.2974 Cas6e CU-H1O3P1 GNIKRCR 2 1.0179203748703 0.0 0,0,0,0,0,0,0 GNIKRCR 845.4654 549.1108 1394.5762 51.76 21.86 24.64 0.00 18.10 0.00 0.00 0.00 -0.0020 2.8 1395.5835 698.2954 465.8660 349.6513 2 +39.118 623.2540 Cse2 U MLTWWGK 2 4.774456024169922 3.456976652145386 0,0,0,345.70,62.76,0,0 MLTwWGK 920.4578 324.0359 1244.4937 36.44 12.42 33.38 0.00 12.90 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 1 39.853 861.3889 Cas5 U LAGPMQAWGQPTFEGTRPTGR 3 11.862678527832031 6.160688877105713 0,0,0,0,0,0,0,0,616.07,0,0,0,0,0,0,0,0,0,0,0,0 LAGPMQAWgQPTFEGTRPTGR 2257.1062 324.0359 2581.1421 43.47 20.67 20.27 0.00 15.70 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 1 39.853 861.3889 DECOY_Cas5 U TGEFTPQGWAQMPGALRGTPR 3 2.125545740127563 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 TGEFTPQGWAQMPGALRGTPR 2257.1062 324.0359 2581.1421 43.47 20.67 20.27 0.00 15.70 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 2 -40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 5.287387371063232 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 35.35 13.70 12.12 0.00 9.76 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 +40.038 1043.4525 Cas7 GU-H2O1 SGYYAQNIGESSLRTIHLAQLR 3 5.287638664245606 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 35.35 13.70 12.12 0.00 9.76 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 1 diff --git a/src/tests/topp/OpenNuXL_5_output.idXML b/src/tests/topp/OpenNuXL_5_output.idXML index bc5dc2f9c2c..7e4aab96963 100644 --- a/src/tests/topp/OpenNuXL_5_output.idXML +++ b/src/tests/topp/OpenNuXL_5_output.idXML @@ -6,7 +6,7 @@ - + @@ -102,9 +102,9 @@ - + - + @@ -112,41 +112,41 @@ - + - + - + - + - - - + + + - + - - + + - - + + - - + + @@ -171,58 +171,58 @@ - + - + - + - - + + - + - - - + + + - + - - + + - + - - + + - + - + - - + + @@ -247,7 +247,7 @@ - + @@ -332,30 +332,30 @@ - + - + - + - + - + - + - - - + + + - + @@ -366,15 +366,15 @@ - + - - + + - - + + @@ -399,39 +399,39 @@ - + - + - + - - + + - - - - - - - - - - - + + + + + + + + + + + - - + + - + @@ -442,15 +442,15 @@ - + - - + + - - + + @@ -475,7 +475,7 @@ - + @@ -558,51 +558,51 @@ - + - + - + - - - - - - - - - + + + + + + + + + - - + + - + - + - - + + - + - - + + - - + + @@ -627,39 +627,39 @@ - + - + - + - + - - - + + + - - - + + + - - - - + + + + - + @@ -670,15 +670,15 @@ - + - - + + - - + + @@ -703,7 +703,7 @@ - + @@ -786,51 +786,51 @@ - + - + - - + + - + - - - + + + - + - - + + - + - - + + - + - - + + - - + + @@ -855,7 +855,7 @@ - + @@ -938,32 +938,32 @@ - + - + - - + + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - - + + @@ -974,15 +974,15 @@ - + - - + + - - + + @@ -1007,7 +1007,7 @@ - + @@ -1090,32 +1090,32 @@ - + - + - - - + + + - + - + - + - + - + - + @@ -1126,15 +1126,15 @@ - + - - + + - - + + @@ -1159,39 +1159,39 @@ - + - + - + - - + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + @@ -1202,15 +1202,15 @@ - + - - + + - - + + @@ -1235,39 +1235,39 @@ - + - + - + - - + + - + - + - + - + - - - + + + - + @@ -1278,15 +1278,15 @@ - + - - + + - - + + @@ -1311,58 +1311,58 @@ - + - + - + - + - - + + - + - - - + + + - - - + + + - + - - + + - - + + - - + + @@ -1387,7 +1387,7 @@ - + @@ -1472,30 +1472,30 @@ - + - + - + - + - + - + - + - + - + @@ -1506,15 +1506,15 @@ - + - - + + - - + + @@ -1539,7 +1539,7 @@ - + diff --git a/src/tests/topp/SimpleSearchEngine_1_out.idXML b/src/tests/topp/SimpleSearchEngine_1_out.idXML index 5e094640f1f..1f7dbbaae66 100644 --- a/src/tests/topp/SimpleSearchEngine_1_out.idXML +++ b/src/tests/topp/SimpleSearchEngine_1_out.idXML @@ -4,7 +4,7 @@ - + @@ -19,14 +19,14 @@ - + - + From 46b7521ed71313655b756c96d43565fafc391467 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 7 May 2020 12:59:00 +0200 Subject: [PATCH 109/471] some style fixes --- src/utils/OpenNuXL.cpp | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1c8d712b06e..8dcfea9643b 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -1489,7 +1489,7 @@ static void scoreXLIons_( public: // initalize tagger with minimum/maximum tag length and +- tolerance ppm - OpenNuXLTagger(float tol = 0.05, size_t min_tag_length = 0, size_t max_tag_length = 65535) + explicit OpenNuXLTagger(float tol = 0.05, size_t min_tag_length = 0, size_t max_tag_length = 65535) { tol_ = tol; min_tag_length_ = min_tag_length; @@ -1624,10 +1624,9 @@ static void scoreXLIons_( int max_size_; public: priority_queue, std::greater> pq; - SmallestElements(size_t size): + explicit SmallestElements(size_t size): max_size_(size) { - pq = priority_queue, std::greater>(); // smallest element at top } void tryAdd(size_t v) @@ -1892,7 +1891,7 @@ static void scoreXLIons_( for (const auto& aa2 : aa2mass2count) { auto& mass2count = aa2.second; - for (const auto m2c : mass2count) + for (const auto& m2c : mass2count) { double current_mass = m2c.first; size_t current_residue_count = m2c.second; @@ -1901,9 +1900,9 @@ static void scoreXLIons_( { cout << aa2.first->getName() << "\t" << current_mass << "\t" << current_residue_count << endl; // aa, mass, count } - double frequency_normalized = (double)current_residue_count / unmodified_residue_count; // frequency relative to unmodified residue #ifdef FILTER_AMBIGIOUS_PEAKS + double frequency_normalized = (double)current_residue_count / unmodified_residue_count; // frequency relative to unmodified residue if (frequency_normalized > 0.5 && frequency_normalized != 1.0) // residue with shift as frequent as unmodified residue { mass2high_frequency_[m2c.first] = frequency_normalized; @@ -1918,14 +1917,14 @@ static void scoreXLIons_( for (const auto& aa2 : aa2mass2count) { auto& mass2count = aa2.second; - for (const auto m2c : mass2count) + for (const auto& m2c : mass2count) { // normalize by counts double current_mass = m2c.first; size_t current_residue_count = m2c.second; size_t unmodified_residue_count = mass2count.begin()->second; double frequency_normalized = (double)current_residue_count / unmodified_residue_count; - cout << aa2.first->getName() << "\t" << current_mass << "\t" << frequency_normalized << endl ; // aa mass count + cout << aa2.first->getName() << "\t" << current_mass << "\t" << frequency_normalized << endl; // aa mass count } } } @@ -3343,7 +3342,7 @@ static void scoreXLIons_( if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) { // fill XL related feature columns with zeros - for (auto s : feature_set) + for (const auto & s : feature_set) { if (s.hasPrefix("NuXL")) ph.setMetaValue("XL_" + s, 0.0); } @@ -3351,7 +3350,7 @@ static void scoreXLIons_( else // XL { // fill linear peptide releated feature columns with zero (after copying them over) - for (auto s : feature_set) + for (const auto& s : feature_set) { if (s.hasPrefix("NuXL")) { @@ -3365,7 +3364,7 @@ static void scoreXLIons_( // we duplicated the feature set auto XL_columns = feature_set; - for (auto s : feature_set) { if (s.hasPrefix("NuXL")) XL_columns.push_back("XL_" + s); } + for (const auto& s : feature_set) { if (s.hasPrefix("NuXL")) XL_columns.push_back("XL_" + s); } feature_set = XL_columns; #endif @@ -3886,7 +3885,7 @@ static void scoreXLIons_( // << "-nested-xval-bins" << "3" //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice // << "-weights" << weights_out.toQString(); - ; + TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); if (exit_code != EXECUTION_OK) From 909af10fb4d1fe85aba5b990f09f4166fbfd34c2 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 7 May 2020 14:52:51 +0200 Subject: [PATCH 110/471] style --- src/utils/OpenNuXL.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 8dcfea9643b..7f470a8948f 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -1895,7 +1895,9 @@ static void scoreXLIons_( { double current_mass = m2c.first; size_t current_residue_count = m2c.second; +#ifdef FILTER_AMBIGIOUS_PEAKS size_t unmodified_residue_count = mass2count.begin()->second; +#endif if (debug_level_ > 0) { cout << aa2.first->getName() << "\t" << current_mass << "\t" << current_residue_count << endl; // aa, mass, count From 2f9be265336aab14a040bd5dd5bfc5dd8feca7b9 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Sun, 10 May 2020 20:24:46 +0200 Subject: [PATCH 111/471] merge against develop --- src/utils/OpenNuXL.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 7f470a8948f..8bd11e90e33 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -5497,7 +5497,7 @@ variable_modifications -0.0944707 { csv_file.addLine(r.getString("\t")); } - const String out_percolator_tsv = File::removeExtension(out_tsv) + "_perc.tsv"; + const String out_percolator_tsv = FileHandler::stripExtension(out_tsv) + "_perc.tsv"; csv_file.store(out_percolator_tsv); } From b20b54410205587975fab20daaea7e3392afe13a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 14 May 2020 12:24:31 +0200 Subject: [PATCH 112/471] added fragment annotation column to tsv --- .../OpenMS/ANALYSIS/RNPXL/RNPxlReport.h | 26 ++-- .../source/ANALYSIS/RNPXL/RNPxlReport.cpp | 118 +++++++++--------- src/utils/OpenNuXL.cpp | 26 +++- 3 files changed, 97 insertions(+), 73 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlReport.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlReport.h index 004073cef90..f4b238d5d6d 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlReport.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlReport.h @@ -50,41 +50,47 @@ namespace OpenMS struct OPENMS_DLLAPI RNPxlReportRow { bool no_id; + + // columns double rt; double original_mz; String accessions; - String RNA; String peptide; + String NA; + Int charge; + double score; + int rank; double best_localization_score; String localization_scores; String best_localization; - Int charge; - double score; double peptide_weight; - double RNA_weight; + double NA_weight; double xl_weight; + StringList meta_values; // the actual values of exported metadata + RNPxlMarkerIonExtractor::MarkerIonsType marker_ions; double abs_prec_error; double rel_prec_error; - RNPxlMarkerIonExtractor::MarkerIonsType marker_ions; double m_H; double m_2H; double m_3H; - double m_4H; - int rank; + double m_4H; + String fragment_annotation; String getString(const String& separator) const; - }; /// create header line struct OPENMS_DLLAPI RNPxlReportRowHeader { - static String getString(const String& separator); + static String getString(const String& separator, const StringList& meta_values_to_export); }; /// create report struct OPENMS_DLLAPI RNPxlReport { - static std::vector annotate(const PeakMap& spectra, std::vector& peptide_ids, double marker_ions_tolerance); + static std::vector annotate(const PeakMap& spectra, + std::vector& peptide_ids, + const StringList& meta_values_to_export, + double marker_ions_tolerance); }; } diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp index f70bb17b2da..7d8a35abb56 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp @@ -43,23 +43,37 @@ namespace OpenMS StringList sl; // rt mz - sl << String::number(rt, 3) << String::number(original_mz, 4); + sl << String::number(rt, 3) + << String::number(original_mz, 4); // id if available if (no_id) { - sl << "" << "" << "" << "" << "" << "" << "" << "" << "" << "" << "" << ""; + for (Size i = 0; i != 12; ++i) sl << ""; } else { - sl << accessions << RNA << peptide << String(charge) << String(score) - << best_localization_score << localization_scores << best_localization - << String::number(peptide_weight, 4) << String::number(RNA_weight, 4) - << String::number(peptide_weight + RNA_weight, 4); + sl << accessions + << peptide + << NA + << String(charge) + << String(score) + << String(rank) + << best_localization_score + << localization_scores + << best_localization + << String::number(peptide_weight, 4) << String::number(NA_weight, 4) + << String::number(peptide_weight + NA_weight, 4); + } + + // write out meta value columns + for (const String& v : meta_values) + { + sl << v; } // marker ions - for (RNPxlMarkerIonExtractor::MarkerIonsType::const_iterator it = marker_ions.begin(); it != marker_ions.end(); ++it) + for (auto it = marker_ions.cbegin(); it != marker_ions.cend(); ++it) { for (Size i = 0; i != it->second.size(); ++i) { @@ -70,8 +84,7 @@ namespace OpenMS // id error and multiple charged mass if (no_id) { - sl << "" << "" << "" - << "" << "" << "" << ""; + for (Size i = 0; i != 7; ++i) sl << ""; } else { @@ -84,19 +97,32 @@ namespace OpenMS << String::number(m_2H, 4) << String::number(m_3H, 4) << String::number(m_4H, 4); - // rank - sl << String(rank); + + sl << fragment_annotation; } return ListUtils::concatenate(sl, separator); } - String RNPxlReportRowHeader::getString(const String& separator) + String RNPxlReportRowHeader::getString(const String& separator, const StringList& meta_values_to_export) { StringList sl; - sl << "#RT" << "original m/z" << "proteins" << "RNA" << "peptide" << "charge" << "score" - << "best localization score" << "localization scores" << "best localization(s)" - << "peptide weight" << "RNA weight" << "cross-link weight"; + sl << "#RT" + << "m/z" + << "proteins" + << "peptide" + << "NA" + << "charge" + << "score" + << "rank" + << "best localization score" + << "localization scores" + << "best localization(s)" + << "peptide weight" + << "NA weight" + << "cross-link weight"; + + for (const String& s : meta_values_to_export) sl << s; // marker ion fields RNPxlMarkerIonExtractor::MarkerIonsType marker_ions = RNPxlMarkerIonExtractor::extractMarkerIons(PeakSpectrum(), 0.0); // call only to generate header entries @@ -107,11 +133,17 @@ namespace OpenMS sl << String(ma.first + "_" + ma.second[i].first); } } - sl << "abs prec. error Da" << "rel. prec. error ppm" << "M+H" << "M+2H" << "M+3H" << "M+4H" << "rank"; + sl << "abs prec. error Da" + << "rel. prec. error ppm" + << "M+H" + << "M+2H" + << "M+3H" + << "M+4H" + << Constants::UserParam::FRAGMENT_ANNOTATION_USERPARAM; return ListUtils::concatenate(sl, separator); } - std::vector RNPxlReport::annotate(const PeakMap& spectra, std::vector& peptide_ids, double marker_ions_tolerance) + std::vector RNPxlReport::annotate(const PeakMap& spectra, std::vector& peptide_ids, const StringList& meta_values_to_export, double marker_ions_tolerance) { std::map map_spectra_to_id; for (Size i = 0; i != peptide_ids.size(); ++i) @@ -159,7 +191,15 @@ namespace OpenMS for (PeptideHit& ph : phs) { ++rank; - // total weight = precursor RNA weight + peptide weight + + for (const String& meta_key : meta_values_to_export) + { + row.meta_values.emplace_back(ph.getMetaValue(meta_key).toString()); + } + + PeptideHit::PeakAnnotation::writePeakAnnotationsString_(row.fragment_annotation, ph.getPeakAnnotations()); + + // total weight = precursor NA weight + peptide weight // this ensures that sequences with additional reported partial loss match the total weight // Note that the partial loss is only relevent on the MS2 and would otherwise be added to the totalweight String sequence_string = ph.getSequence().toString(); @@ -200,12 +240,12 @@ namespace OpenMS row.rt = rt; row.original_mz = mz; row.accessions = protein_accessions; - row.RNA = rna_name; + row.NA = rna_name; row.peptide = ph.getSequence().toString(); row.charge = charge; row.score = ph.getScore(); row.peptide_weight = peptide_weight; - row.RNA_weight = rna_weight; + row.NA_weight = rna_weight; row.xl_weight = peptide_weight + rna_weight; row.rank = rank; @@ -244,44 +284,6 @@ namespace OpenMS ph.setMetaValue("NuXL:z3 mass", (double)weight_z3); ph.setMetaValue("NuXL:z4 mass", (double)weight_z4); csv_rows.push_back(row); - - -/* - // In the last annotation step we add the oligo as delta mass modification - // to get the proper theoretical mass annotated in the PeptideHit - // Try to add it to the C- then N-terminus. - // If already modified search for an unmodified amino acid and add it there - if (rna_weight > 0) - { - AASequence aa = ph.getSequence(); - const String seq = ph.getSequence().toString(); - - if (!aa.hasCTerminalModification()) - { - aa = AASequence::fromString(seq + ".[" + String(rna_weight + Residue::getInternalToCTerm().getMonoWeight()) + "]"); - ph.setSequence(aa); - } - else if (!aa.hasNTerminalModification()) - { - aa = AASequence::fromString("[" + String(rna_weight + Residue::getInternalToNTerm().getMonoWeight()) + "]." + seq); - ph.setSequence(aa); - } - else // place it anywhere - { - Size index(0); - for (auto & a : aa) - { - if (!a.isModified()) - { - aa.setModification(index, "[+" + String(rna_weight) + "]"); - break; - } - ++index; - } - ph.setSequence(aa); - } - } -*/ } } } diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 8bd11e90e33..25c9804b383 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -2092,7 +2092,10 @@ static void scoreXLIons_( dist_file << mz << "\t" << peak_density.getBinIntensity(mz) << "\n"; } dist_file.close(); - MzMLFile().store("debug_filtering.mzML", exp); + + #ifdef DEBUG_OpenNuXL + MzMLFile().store("debug_filtering.mzML", exp); + #endif } void filterTopNAnnotations_(vector>& ahs, const Size top_hits) @@ -4846,8 +4849,21 @@ static void scoreXLIons_( } } + StringList meta_values_to_export; + meta_values_to_export.push_back("NuXL:total_loss_score"); + meta_values_to_export.push_back("NuXL:partial_loss_score"); + meta_values_to_export.push_back("CountSequenceIsTop"); + meta_values_to_export.push_back("CountSequenceCharges"); + meta_values_to_export.push_back("CountSequenceIsXL"); + meta_values_to_export.push_back("CountSequenceIsPeptide"); + meta_values_to_export.push_back("NuXL:MIC"); + meta_values_to_export.push_back("NuXL:pl_pc_MIC"); + meta_values_to_export.push_back("NuXL:pl_MIC"); + meta_values_to_export.push_back("nr_candidates"); + meta_values_to_export.push_back("isotope_error"); + // annotate RNPxl related information to hits and create report - vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); + vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, meta_values_to_export, marker_ions_tolerance); #ifdef ANNOTATED_QUANTILES for (Size scan_index = 0; scan_index != peptide_ids.size(); ++scan_index) @@ -5486,13 +5502,13 @@ variable_modifications -0.0944707 IDFilter::removeUnreferencedProteins(protein_ids, peptide_ids); // annotate RNPxl related information to hits and create report - vector csv_rows_percolator = RNPxlReport::annotate(spectra, peptide_ids, marker_ions_tolerance); + vector csv_rows_percolator = RNPxlReport::annotate(spectra, peptide_ids, meta_values_to_export, marker_ions_tolerance); // save report if (!out_tsv.empty()) { TextFile csv_file; - csv_file.addLine(RNPxlReportRowHeader().getString("\t")); + csv_file.addLine(RNPxlReportRowHeader().getString("\t", meta_values_to_export)); for (const RNPxlReportRow r : csv_rows_percolator) { csv_file.addLine(r.getString("\t")); @@ -5576,7 +5592,7 @@ variable_modifications -0.0944707 if (!out_tsv.empty()) { TextFile csv_file; - csv_file.addLine(RNPxlReportRowHeader().getString("\t")); + csv_file.addLine(RNPxlReportRowHeader().getString("\t", meta_values_to_export)); for (Size i = 0; i != csv_rows.size(); ++i) { csv_file.addLine(csv_rows[i].getString("\t")); From 60d587c7e82231ab1b8310d9654232e6b8a7efaa Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 20 May 2020 17:00:18 +0200 Subject: [PATCH 113/471] fix deisotoper and output primary ms run path --- .../FILTERING/DATAREDUCTION/Deisotoper.cpp | 7 ++++--- src/utils/OpenNuXL.cpp | 19 +++++++++++++------ 2 files changed, 17 insertions(+), 9 deletions(-) diff --git a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp index dd76647ff6b..d71dd90eb37 100644 --- a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp +++ b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp @@ -67,9 +67,6 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, OPENMS_PRETTY_FUNCTION, "Minimum/maximum number of isotopic peaks must be at least 2 (and min_isopeaks <= max_isopeaks)."); } - - if (spec.empty()) { return; } - Size charge_index(0); Size iso_peak_count_index(0); @@ -81,6 +78,7 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, spec.getIntegerDataArrays().back().setName("charge"); charge_index = spec.getIntegerDataArrays().size()-1; } + // reserve integer data array to store number of isotopic peaks for each isotopic pattern if (annotate_iso_peak_count) { @@ -89,6 +87,9 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, iso_peak_count_index = spec.getIntegerDataArrays().size()-1; } + // in case of an empty spectrum we still create the integer data arrays and return. + if (spec.empty()) { return; } + // during discovery phase, work on a constant reference (just to make sure we do not modify spec) const MSSpectrum& old_spectrum = spec; diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 25c9804b383..f33c1fd2655 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -1964,12 +1964,11 @@ static void scoreXLIons_( ThresholdMower threshold_mower_filter; threshold_mower_filter.filterPeakMap(exp); -#ifdef _OPENMP #pragma omp parallel for -#endif for (SignedSize exp_index = 0; exp_index < (SignedSize)exp.size(); ++exp_index) { MSSpectrum & spec = exp[exp_index]; + // sort by mz spec.sortByPosition(); @@ -1983,7 +1982,9 @@ static void scoreXLIons_( single_charge_spectra, annotate_charge, false, // no iso peak count annotation - false); // no isotope model + true, // decreasing isotope model + 2, // enforce only starting from second peak + true); // add up intensities } @@ -2006,7 +2007,9 @@ static void scoreXLIons_( NLargest nlargest_filter = NLargest(400); + #ifdef DEBUG_OpenNuXL BinnedSpectrum peak_density(MSSpectrum(), 0.05, false, 0, 0); + #endif #pragma omp parallel for for (SignedSize exp_index = 0; exp_index < (SignedSize)exp.size(); ++exp_index) @@ -2069,11 +2072,13 @@ static void scoreXLIons_( cout << spec[i].getMZ() << "\t" << spec[i].getIntensity() << "\t" << ia[i] << endl; #endif +#ifdef DEBUG_OpenNuXL BinnedSpectrum bs(spec, 0.05, false, 0, 0); bs.getBins().coeffs().cwiseMax(1); #pragma omp critical (peak_density_access) peak_density.getBins() += bs.getBins(); +#endif // calculate TIC and store in float data array double TIC = std::accumulate(spec.begin(), spec.end(), 0.0, @@ -2084,6 +2089,7 @@ static void scoreXLIons_( spec.getFloatDataArrays()[0].setName("TIC"); } +#ifdef DEBUG_OpenNuXL ofstream dist_file; dist_file.open(getStringOption_("in") + ".fragment_dist.csv"); dist_file << "m/z\tfragments" << "\n"; @@ -2093,9 +2099,8 @@ static void scoreXLIons_( } dist_file.close(); - #ifdef DEBUG_OpenNuXL - MzMLFile().store("debug_filtering.mzML", exp); - #endif + MzMLFile().store("debug_filtering.mzML", exp); +#endif } void filterTopNAnnotations_(vector>& ahs, const Size top_hits) @@ -4821,6 +4826,8 @@ static void scoreXLIons_( nr_candidates); progresslogger.endProgress(); + protein_ids[0].setPrimaryMSRunPath({"file://" + File::basename(in_mzml)}); + // reindex ids PeptideIndexing indexer; Param param_pi = indexer.getParameters(); From b646b5b9d3b6c574a81182767143b01377a1e52b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 3 Jun 2020 14:16:20 +0200 Subject: [PATCH 114/471] [feature] remove coeluting and high spectral similarity MS2 --- .../ID/SimpleSearchEngineAlgorithm.cpp | 35 ++++--- src/utils/OpenNuXL.cpp | 92 +++++++++++++++++-- 2 files changed, 105 insertions(+), 22 deletions(-) diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index 0b066776146..23fa2cd20f1 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -164,8 +164,20 @@ namespace OpenMS fragment_mass_tolerance_unit_ = param_.getValue("fragment:mass_tolerance_unit"); modifications_fixed_ = param_.getValue("modifications:fixed"); + set fixed_unique(modifications_fixed_.begin(), modifications_fixed_.end()); + if (fixed_unique.size() != modifications_fixed_.size()) + { + OPENMS_LOG_WARN << "Duplicate fixed modification provided. Making them unique." << endl; + modifications_fixed_.assign(fixed_unique.begin(), fixed_unique.end()); + } modifications_variable_ = param_.getValue("modifications:variable"); + set var_unique(modifications_variable_.begin(), modifications_variable_.end()); + if (var_unique.size() != modifications_variable_.size()) + { + OPENMS_LOG_WARN << "Duplicate variable modification provided. Making them unique." << endl; + modifications_variable_.assign(var_unique.begin(), var_unique.end()); + } modifications_max_variable_mods_per_peptide_ = param_.getValue("modifications:variable_max_per_peptide"); @@ -361,6 +373,14 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, search_parameters.precursor_mass_tolerance_ppm = precursor_mass_tolerance_unit_ppm == "ppm"; search_parameters.fragment_mass_tolerance_ppm = fragment_mass_tolerance_unit_ppm == "ppm"; search_parameters.digestion_enzyme = *ProteaseDB::getInstance()->getEnzyme(enzyme); + + // for post-processing + search_parameters.setMetaValue("feature_extractor", "TOPP_PSMFeatureExtractor"); + StringList feature_set{"score"}; + if (annotation_fragment_error_ppm) feature_set.push_back(Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM); + search_parameters.setMetaValue("extra_features", ListUtils::concatenate(feature_set, ",")); + + protein_ids[0].setSearchParameters(search_parameters); protein_ids[0].setSearchParameters(std::move(search_parameters)); } @@ -371,21 +391,6 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, bool precursor_mass_tolerance_unit_ppm = (precursor_mass_tolerance_unit_ == "ppm"); bool fragment_mass_tolerance_unit_ppm = (fragment_mass_tolerance_unit_ == "ppm"); - set fixed_unique(modifications_fixed_.begin(), modifications_fixed_.end()); - - if (fixed_unique.size() != modifications_fixed_.size()) - { - cout << "duplicate fixed modification provided." << endl; - return ExitCodes::ILLEGAL_PARAMETERS; - } - - set var_unique(modifications_variable_.begin(), modifications_variable_.end()); - if (var_unique.size() != modifications_variable_.size()) - { - cout << "duplicate variable modification provided." << endl; - return ExitCodes::ILLEGAL_PARAMETERS; - } - ModifiedPeptideGenerator::MapToResidueType fixed_modifications = ModifiedPeptideGenerator::getModifications(modifications_fixed_); ModifiedPeptideGenerator::MapToResidueType variable_modifications = ModifiedPeptideGenerator::getModifications(modifications_variable_); diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index f33c1fd2655..8c4d5881a06 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -70,7 +70,7 @@ // preprocessing and filtering #include - +#include #include #include #include @@ -78,6 +78,9 @@ #include #include +#include +#include + #include #include #include @@ -557,7 +560,7 @@ class OpenNuXL : registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); registerStringList_("filter", "", {"filter_pc_mass_error", "autotune", "idfilter"}, "Filtering steps applied to results.", false, true); - setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune", "idfilter"}); + setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune", "idfilter", "spectrumclusterfilter"}); } @@ -3839,6 +3842,7 @@ static void scoreXLIons_( bool filter_bad_partial_loss_scores = find(filter.begin(), filter.end(), "filter_bad_partial_loss_scores") != filter.end(); bool autotune = find(filter.begin(), filter.end(), "autotune") != filter.end(); bool idfilter = find(filter.begin(), filter.end(), "idfilter") != filter.end(); + bool spectrumclusterfilter = find(filter.begin(), filter.end(), "spectrumclusterfilter") != filter.end(); // autotune (only works if non-XL peptides present) set skip_peptide_spectrum; @@ -3853,10 +3857,10 @@ static void scoreXLIons_( p.setValue("fragment:mass_tolerance", fragment_mass_tolerance); p.setValue("fragment:mass_tolerance_unit", getStringOption_("fragment:mass_tolerance_unit")); StringList var_mods = getStringList_("modifications:variable"); - if (find(var_mods.begin(), var_mods.end(), "Phospho (S)") != var_mods.end()) { var_mods.push_back("Phospho (S)"); } - if (find(var_mods.begin(), var_mods.end(), "Phospho (T)") != var_mods.end()) { var_mods.push_back("Phospho (T)"); } - if (find(var_mods.begin(), var_mods.end(), "Phospho (Y)") != var_mods.end()) { var_mods.push_back("Phospho (Y)"); } - if (find(var_mods.begin(), var_mods.end(), "Oxidation (M)") != var_mods.end()) { var_mods.push_back("Oxidation (M)"); } + if (find(var_mods.begin(), var_mods.end(), "Phospho (S)") == var_mods.end()) { var_mods.push_back("Phospho (S)"); } + if (find(var_mods.begin(), var_mods.end(), "Phospho (T)") == var_mods.end()) { var_mods.push_back("Phospho (T)"); } + if (find(var_mods.begin(), var_mods.end(), "Phospho (Y)") == var_mods.end()) { var_mods.push_back("Phospho (Y)"); } + if (find(var_mods.begin(), var_mods.end(), "Oxidation (M)") == var_mods.end()) { var_mods.push_back("Oxidation (M)"); } StringList fixed_mods = getStringList_("modifications:fixed"); p.setValue("modifications:fixed", fixed_mods); p.setValue("modifications:variable", var_mods); @@ -3879,6 +3883,8 @@ static void scoreXLIons_( bool sufficient_PSMs_for_score_recalibration = pep_ids.size() > 1000; if (!percolator_executable.empty() && sufficient_PSMs_for_score_recalibration) // only try to call percolator if we have some PSMs { + IdXMLFile().store(out_idxml, prot_ids, pep_ids); + // run percolator on idXML String perc_out = out_idxml; perc_out.substitute(".idXML", "_sse_perc.idXML"); @@ -3892,7 +3898,7 @@ static void scoreXLIons_( << "-train-best-positive" << "-score_type" << "q-value" << "-post-processing-tdc"; -// << "-nested-xval-bins" << "3" +// << "-nested-xval-bins" << "3"; //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice // << "-weights" << weights_out.toQString(); @@ -3926,6 +3932,78 @@ static void scoreXLIons_( skip_peptide_spectrum.insert((String)pi.getMetaValue("spectrum_reference")); // get native id } } + + if (spectrumclusterfilter) + { + Size skipped_similar_spectra(0); + // load MS2 map + PeakMap spectra; + MzMLFile f; + f.setLogType(log_type_); + PeakFileOptions options; + options.clearMSLevels(); + options.addMSLevel(2); + f.getOptions() = options; + f.load(in_mzml, spectra); + spectra.sortSpectra(true); + SpectrumLookup lookup; + lookup.readSpectra(spectra); + // build kdtree + Param p; + p.setValue("rt_tol", 60.0); + p.setValue("mz_tol", precursor_mass_tolerance); + p.setValue("mz_unit", "ppm"); + FeatureMap fmap; + for (Size i = 0; i != spectra.size(); ++i) + { + const MSSpectrum& s = spectra[i]; + + Feature feat; + feat.setMZ(s.getPrecursors()[0].getMZ()); + feat.setRT(s.getRT()); + feat.setMetaValue("native_id", s.getNativeID()); + fmap.push_back(feat); + } + vector fmaps; + fmaps.push_back(std::move(fmap)); + KDTreeFeatureMaps kdtree(fmaps, p); + + // filter all coeluting MS2 with high spectral similarity to identified one + for (const auto& pi : perc_pep_ids) + { + String this_native_id = (String)pi.getMetaValue("spectrum_reference"); + + std::vector result_indices; + + // find neighbors + double m = Math::ppmToMass(precursor_mass_tolerance, pi.getMZ()); + kdtree.queryRegion(pi.getRT() - 60.0, pi.getRT() + 60.0, pi.getMZ() - m, pi.getMZ() + m, result_indices); + + if (result_indices.size() > 1) + { + for (Size ix : result_indices) + { + auto f = kdtree.feature(ix); + const String other_native_id = f->getMetaValue("native_id"); + + // skip self-comparison and already identified spectra + if (this_native_id == other_native_id || skip_peptide_spectrum.count(other_native_id) > 0) continue; + + const MSSpectrum& this_spec = spectra[lookup.findByNativeID(this_native_id)]; + const MSSpectrum& other_spec = spectra[lookup.findByNativeID(other_native_id)]; + BinnedSpectrum bs1 (this_spec, BinnedSpectrum::DEFAULT_BIN_WIDTH_LOWRES, false, 1, BinnedSpectrum::DEFAULT_BIN_OFFSET_LOWRES); + BinnedSpectrum bs2 (other_spec, BinnedSpectrum::DEFAULT_BIN_WIDTH_LOWRES, false, 1, BinnedSpectrum::DEFAULT_BIN_OFFSET_LOWRES); + const float contrast_angle = BinnedSpectralContrastAngle()(bs1, bs2); + if (contrast_angle > 0.9) + { + skip_peptide_spectrum.insert(other_native_id); + skipped_similar_spectra++; + } + } + } + } + cout << "Excluded coelution precursors with high spectral similarity: " << skipped_similar_spectra << endl; + } } ////////// end percolator part From e1b0a70fa30662f688966dfc0354c1a63427e12b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 5 Jun 2020 09:47:35 +0200 Subject: [PATCH 115/471] mass calibration --- src/utils/OpenNuXL.cpp | 42 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 8c4d5881a06..3e890229f57 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -69,6 +69,7 @@ #include // preprocessing and filtering +#include #include #include #include @@ -560,7 +561,7 @@ class OpenNuXL : registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); registerStringList_("filter", "", {"filter_pc_mass_error", "autotune", "idfilter"}, "Filtering steps applied to results.", false, true); - setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune", "idfilter", "spectrumclusterfilter"}); + setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune", "idfilter", "spectrumclusterfilter", "pcrecalibration"}); } @@ -3843,6 +3844,9 @@ static void scoreXLIons_( bool autotune = find(filter.begin(), filter.end(), "autotune") != filter.end(); bool idfilter = find(filter.begin(), filter.end(), "idfilter") != filter.end(); bool spectrumclusterfilter = find(filter.begin(), filter.end(), "spectrumclusterfilter") != filter.end(); + bool pcrecalibration = find(filter.begin(), filter.end(), "pcrecalibration") != filter.end(); + + InternalCalibration ic; // only filled if pcrecalibration is set and there are enough calibrants // autotune (only works if non-XL peptides present) set skip_peptide_spectrum; @@ -4052,6 +4056,12 @@ static void scoreXLIons_( { OPENMS_LOG_INFO << "autotune: too few non-cross-linked peptides found. Will keep parameters as-is." << endl; } + + if (pcrecalibration) + { + ic.setLogType(log_type_); + ic.fillCalibrants(pep_ids, precursor_mass_tolerance); + } } OPENMS_LOG_INFO << "IDFilter excludes " << skip_peptide_spectrum.size() << " spectra." << endl; @@ -4186,6 +4196,36 @@ static void scoreXLIons_( f.load(in_mzml, spectra); spectra.sortSpectra(true); + // only executed if we have a pre-search with enough calibrants + if (ic.getCalibrationPoints().size() > 1) + { + MZTrafoModel::MODELTYPE md = MZTrafoModel::QUADRATIC; + bool use_RANSAC = true; + + Size RANSAC_initial_points = (md == MZTrafoModel::LINEAR) ? 2 : 3; + Math::RANSACParam p(RANSAC_initial_points, 70, 10, 30, true); // TODO: check defaults (taken from tool) + MZTrafoModel::setRANSACParams(p); + + // these limits are a little loose, but should prevent grossly wrong models without burdening the user with yet another parameter. + MZTrafoModel::setCoefficientLimits(25.0, 25.0, 0.5); + + IntList ms_level = {1}; + double rt_chunk = 300.0; // 5 minutes covered by each linear model + String qc_residual_path, qc_residual_png_path; + + if (!ic.calibrate(spectra, ms_level, md, rt_chunk, use_RANSAC, + 10.0, + 5.0, + "", + "", + qc_residual_path, + qc_residual_png_path, + "Rscript")) + { + OPENMS_LOG_WARN << "\nCalibration failed. See error message above!" << std::endl; + } + } + progresslogger.startProgress(0, 1, "Filtering spectra..."); const bool convert_to_single_charge = false; // whether to convert fragment peaks with isotopic patterns to single charge preprocessSpectra_(spectra, From ba6566f128949631d3e3edbfc3a4dce99efa76bb Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 11 Jun 2020 10:07:26 +0200 Subject: [PATCH 116/471] precursor correction using features implemented --- .../CALIBRATION/PrecursorCorrection.cpp | 16 ++-- src/utils/OpenNuXL.cpp | 79 +++++++++++++++++++ 2 files changed, 90 insertions(+), 5 deletions(-) diff --git a/src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp b/src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp index 9a8d5c08a0d..480c28f3874 100644 --- a/src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp +++ b/src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp @@ -56,11 +56,8 @@ namespace OpenMS { for (Size i = 0; i != exp.size(); ++i) { - vector pcs = exp[i].getPrecursors(); - if (pcs.empty()) - { - continue; - } + const vector& pcs = exp[i].getPrecursors(); + if (pcs.empty()) { continue; } vector pcs_rt(pcs.size(), exp[i].getRT()); copy(pcs.begin(), pcs.end(), back_inserter(precursors)); copy(pcs_rt.begin(), pcs_rt.end(), back_inserter(precursors_rt)); @@ -252,10 +249,12 @@ namespace OpenMS int debug_level) { set corrected_precursors; + // for each precursor/MS2 find all features that are in the given tolerance window (bounding box + rt tolerances) // if believe_charge is set, only add features that match the precursor charge map > scan_idx_to_feature_idx; + size_t overlap_checks(0); for (Size scan = 0; scan != exp.size(); ++scan) { // skip non-tandem mass spectra @@ -271,6 +270,7 @@ namespace OpenMS // feature is incompatible if believe_charge is set and charges don't match if (believe_charge && features[f].getCharge() != pc_charge) continue; + ++overlap_checks; // check if precursor/MS2 position overlap with feature if (overlaps_(features[f], rt, pc_mz, rt_tolerance_s)) { @@ -279,6 +279,12 @@ namespace OpenMS } } + if (debug_level > 0) + { + OPENMS_LOG_INFO << "Total number of overlap checks: " << overlap_checks << endl; + OPENMS_LOG_INFO << "Number of precursors with overlapping features: " << scan_idx_to_feature_idx.size() << endl; + } + // filter sets to retain compatible features: // if precursor_mz = feature_mz + n * feature_charge (+/- mz_tolerance) a feature is compatible, others are removed from the set for (map >::iterator it = scan_idx_to_feature_idx.begin(); it != scan_idx_to_feature_idx.end(); ++it) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 3e890229f57..f130bd140f4 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -97,6 +97,7 @@ #include #include +#include #include #include @@ -3808,6 +3809,74 @@ static void scoreXLIons_( return tags; } + ExitCodes correctPrecursors(MSExperiment& ms_centroided) + { + //------------------------------------------------------------- + // HighRes Precursor Mass Correction + //------------------------------------------------------------- + std::vector deltaMZs, mzs, rts; + std::set corrected_to_highest_intensity_peak = PrecursorCorrection::correctToHighestIntensityMS1Peak( + ms_centroided, + 0.01, // check if we can estimate this from data (here it is given in m/z not ppm) + false, // is ppm = false + deltaMZs, + mzs, + rts + ); + writeLog_("Info: Corrected " + String(corrected_to_highest_intensity_peak.size()) + " precursors."); + if (!deltaMZs.empty()) + { + vector deltaMZs_ppm, deltaMZs_ppmabs; + for (Size i = 0; i != deltaMZs.size(); ++i) + { + deltaMZs_ppm.push_back(Math::getPPM(mzs[i], mzs[i] + deltaMZs[i])); + deltaMZs_ppmabs.push_back(Math::getPPMAbs(mzs[i], mzs[i] + deltaMZs[i])); + } + + double median = Math::median(deltaMZs_ppm.begin(), deltaMZs_ppm.end()); + double MAD = Math::MAD(deltaMZs_ppm.begin(), deltaMZs_ppm.end(), median); + double median_abs = Math::median(deltaMZs_ppmabs.begin(), deltaMZs_ppmabs.end()); + double MAD_abs = Math::MAD(deltaMZs_ppmabs.begin(), deltaMZs_ppmabs.end(), median_abs); + writeLog_("Precursor correction to highest intensity peak:\n median delta m/z = " + + String(median) + " ppm MAD = " + String(MAD) + + "\n median delta m/z (abs.) = " + String(median_abs) + + " ppm MAD = " + String(MAD_abs)); + } + + FeatureMap features; + { + MSExperiment e(ms_centroided); // FFM seems to delete passed spectra + FeatureFinderMultiplexAlgorithm algorithm; + Param p = algorithm.getParameters(); + p.setValue("algorithm:labels", ""); // label-free + p.setValue("algorithm:charge", "2:5"); + p.setValue("algorithm:rt_typical", 30.0); + p.setValue("algorithm:rt_band", 3.0); // max 3 seconds shifts between isotopic traces + p.setValue("algorithm:rt_min", 4.0); + p.setValue("algorithm:spectrum_type", "centroid"); + algorithm.setParameters(p); + algorithm.run(e, true); + features = algorithm.getFeatureMap(); + writeLog_("Detected peptides: " + String(features.size())); + } + + set correct_to_nearest_feature = PrecursorCorrection::correctToNearestFeature( + features, + ms_centroided, + 20.0, + 0.01, + false, + true, + false, + false, + 3, + 10); + writeLog_("Precursor correction to feature:\n succesful in = " + + String(correct_to_nearest_feature.size()) + " cases."); + + return EXECUTION_OK; + } + ExitCodes main_(int, const char**) override { ProgressLogger progresslogger; @@ -3846,6 +3915,16 @@ static void scoreXLIons_( bool spectrumclusterfilter = find(filter.begin(), filter.end(), "spectrumclusterfilter") != filter.end(); bool pcrecalibration = find(filter.begin(), filter.end(), "pcrecalibration") != filter.end(); + if (pcrecalibration) + { + MSExperiment e; + MzMLFile().load(in_mzml, e); + correctPrecursors(e); + in_mzml = FileHandler::stripExtension(in_mzml) + "_pc.mzML"; + OPENMS_LOG_INFO << "Writing calibrated file to: " << in_mzml << endl; + MzMLFile().store(in_mzml, e); + } + InternalCalibration ic; // only filled if pcrecalibration is set and there are enough calibrants // autotune (only works if non-XL peptides present) From 116fdad6bbef90ac2abfa1957ee47a62f2fe9333 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 12 Jun 2020 10:05:39 +0200 Subject: [PATCH 117/471] correct gloabal fragment error --- src/utils/OpenNuXL.cpp | 59 +++++++++++++++++++++++++++++++++--------- 1 file changed, 47 insertions(+), 12 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index f130bd140f4..37800cfb7b6 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -563,9 +563,14 @@ class OpenNuXL : registerStringList_("filter", "", {"filter_pc_mass_error", "autotune", "idfilter"}, "Filtering steps applied to results.", false, true); setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune", "idfilter", "spectrumclusterfilter", "pcrecalibration"}); + + + registerDoubleOption_("window_size", "", 100.0, "Peak window for spectra precprocessing.", false, true); + registerIntOption_("peak_count", "", 20, "Retained peaks in peak window.", false, true); } + // bad score or less then two peaks matching and less than 1% explained signal static bool badTotalLossScore(float hyperScore, float tlss_Morph, float tlss_modds, float tlss_total_MIC) { @@ -1962,7 +1967,9 @@ static void scoreXLIons_( double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, - bool annotate_charge) + bool annotate_charge, + double window_size, + size_t peakcount) { // filter MS2 map // remove 0 intensities @@ -2005,8 +2012,8 @@ static void scoreXLIons_( // filter settings WindowMower window_mower_filter; Param filter_param = window_mower_filter.getParameters(); - filter_param.setValue("windowsize", 100.0, "The size of the sliding window along the m/z axis."); - filter_param.setValue("peakcount", 20, "The number of peaks that should be kept."); + filter_param.setValue("windowsize", window_size, "The size of the sliding window along the m/z axis."); + filter_param.setValue("peakcount", peakcount, "The number of peaks that should be kept."); filter_param.setValue("movetype", "jump", "Whether sliding window (one peak steps) or jumping window (window size steps) should be used."); window_mower_filter.setParameters(filter_param); @@ -3927,8 +3934,11 @@ static void scoreXLIons_( InternalCalibration ic; // only filled if pcrecalibration is set and there are enough calibrants + // autotune (only works if non-XL peptides present) set skip_peptide_spectrum; + double global_fragment_error(0); + if (autotune || idfilter) { SimpleSearchEngineAlgorithm sse; @@ -3971,8 +3981,9 @@ static void scoreXLIons_( // run percolator on idXML String perc_out = out_idxml; perc_out.substitute(".idXML", "_sse_perc.idXML"); -// String weights_out = out_idxml; -// weights_out.substitute(".idXML", "_sse.weights"); + + String weights_out = out_idxml; + weights_out.substitute(".idXML", "_sse.weights"); QStringList process_params; process_params << "-in" << out_idxml.toQString() @@ -3980,10 +3991,10 @@ static void scoreXLIons_( << "-percolator_executable" << percolator_executable.toQString() << "-train-best-positive" << "-score_type" << "q-value" - << "-post-processing-tdc"; + << "-post-processing-tdc" + << "-weights" << weights_out.toQString(); // << "-nested-xval-bins" << "3"; //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice -// << "-weights" << weights_out.toQString(); TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); @@ -4100,6 +4111,7 @@ static void scoreXLIons_( if (pep_ids.size() > 100) { + vector median_fragment_error_ppm_abs; vector median_fragment_error_ppm; vector precursor_error_ppm; for (const auto& pi : pep_ids) @@ -4108,18 +4120,22 @@ static void scoreXLIons_( if (ph.metaValueExists(Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM)) { //cout << ph.getMetaValue("median_fragment_error_ppm") << endl; - median_fragment_error_ppm.push_back(fabs((double)ph.getMetaValue(Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM))); + double fragment_error = (double)ph.getMetaValue(Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM); + median_fragment_error_ppm_abs.push_back(fabs(fragment_error)); + median_fragment_error_ppm.push_back(fragment_error); } if (ph.metaValueExists(Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM)) { precursor_error_ppm.push_back((double)ph.getMetaValue(Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM)); } } + sort(median_fragment_error_ppm_abs.begin(), median_fragment_error_ppm_abs.end()); sort(median_fragment_error_ppm.begin(), median_fragment_error_ppm.end()); sort(precursor_error_ppm.begin(), precursor_error_ppm.end()); // use 68-percentile as in identipy - double new_fragment_mass_tolerance = 4.0 * median_fragment_error_ppm[median_fragment_error_ppm.size() * 0.68]; + double new_fragment_mass_tolerance = 4.0 * median_fragment_error_ppm_abs[median_fragment_error_ppm_abs.size() * 0.68]; + global_fragment_error = median_fragment_error_ppm[median_fragment_error_ppm_abs.size() * 0.5]; // median of all fragment errors double left_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.005]; double median_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.5]; double right_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.995]; @@ -4129,6 +4145,7 @@ static void scoreXLIons_( fragment_mass_tolerance = new_fragment_mass_tolerance; // set new fragment mass tolerance } cout << "New fragment mass tolerance (ppm): " << new_fragment_mass_tolerance << endl; + cout << "Global fragment mass shift (ppm): " << global_fragment_error << endl; cout << "Estimated precursor mass tolerance (ppm): " << left_precursor_mass_tolerance << "\t" << median_precursor_mass_tolerance << "\t" << right_precursor_mass_tolerance << endl; } else @@ -4140,6 +4157,22 @@ static void scoreXLIons_( { ic.setLogType(log_type_); ic.fillCalibrants(pep_ids, precursor_mass_tolerance); + if (global_fragment_error != 0) + { + PeakMap spectra; + MzMLFile f; + f.load(in_mzml, spectra); + spectra.sortSpectra(true); + for (auto & s : spectra) + { + if (s.getMSLevel() != 2) continue; + for (auto & p : s) + { + p.setMZ(p.getMZ() - Math::ppmToMass(global_fragment_error, p.getMZ())); // correct global fragment error + } + } + f.store(in_mzml, spectra); + } } } @@ -4278,7 +4311,7 @@ static void scoreXLIons_( // only executed if we have a pre-search with enough calibrants if (ic.getCalibrationPoints().size() > 1) { - MZTrafoModel::MODELTYPE md = MZTrafoModel::QUADRATIC; + MZTrafoModel::MODELTYPE md = MZTrafoModel::LINEAR; bool use_RANSAC = true; Size RANSAC_initial_points = (md == MZTrafoModel::LINEAR) ? 2 : 3; @@ -4307,11 +4340,13 @@ static void scoreXLIons_( progresslogger.startProgress(0, 1, "Filtering spectra..."); const bool convert_to_single_charge = false; // whether to convert fragment peaks with isotopic patterns to single charge + const double window_size = getDoubleOption_("window_size"); + const size_t peak_count = getIntOption_("peak_count"); preprocessSpectra_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, convert_to_single_charge, - true); // annotate charge + true, window_size, peak_count); // annotate charge progresslogger.endProgress(); progresslogger.startProgress(0, 1, "Calculate Nucleotide Tags..."); @@ -4979,7 +5014,7 @@ static void scoreXLIons_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, false, // no single charge (false) - true); // annotate charge (true) + true, window_size, peak_count); // annotate charge (true) calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); progresslogger.startProgress(0, 1, "localization..."); From a2f1c02c99c55ab5372402364d21583b6dd11262 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 17 Jun 2020 12:30:29 +0200 Subject: [PATCH 118/471] optimized number of peaks --- src/utils/OpenNuXL.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 37800cfb7b6..b38524f2038 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -565,7 +565,7 @@ class OpenNuXL : setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune", "idfilter", "spectrumclusterfilter", "pcrecalibration"}); - registerDoubleOption_("window_size", "", 100.0, "Peak window for spectra precprocessing.", false, true); + registerDoubleOption_("window_size", "", 75.0, "Peak window for spectra precprocessing.", false, true); registerIntOption_("peak_count", "", 20, "Retained peaks in peak window.", false, true); } From b88cecace8f9a17a98821dd3320455188d3ee4cd Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 22 Jul 2020 10:28:00 +0200 Subject: [PATCH 119/471] fast mass tag calculation --- src/utils/OpenNuXL.cpp | 43 +++++++++++++++++++++++++++++++++++++----- 1 file changed, 38 insertions(+), 5 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index b38524f2038..dbf1737a856 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -127,10 +127,12 @@ using namespace boost::accumulators; //#define FILTER_BAD_SCORES_ID_TAGS filter out some good hits //#define FILTER_AMBIGIOUS_PEAKS //#define FILTER_NO_ARBITRARY_TAG_PRESENT +#define CALCULATE_LONGEST_TAG +//#define MODDS_ON_ABY_IONS_ONLY //#define SVM_RECALIBRATE //#define FILTER_RANKS 1 //#define CALCULATE_NUCLEOTIDE_TAGS 1 -//#define DONT_ACCUMULATE_PARTIAL_ION_SCORES 1 +#define DONT_ACCUMULATE_PARTIAL_ION_SCORES 1 #ifdef ANNOTATED_QUANTILES typedef accumulator_set > quantile_accu_t; @@ -969,19 +971,19 @@ class OpenNuXL : const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000; +#ifdef MODDS_ON_ABY_IONS_ONLY modds = matchOddsScore_(total_loss_template_z1_b_ions.size() + total_loss_template_z1_y_ions.size(), fragment_mass_tolerance_Da, exp_spectrum.size(), exp_spectrum.back().getMZ(), (int)Morph); - -/* +#else modds = matchOddsScore_(comparisons, fragment_mass_tolerance_Da, exp_spectrum.size(), exp_spectrum.back().getMZ(), matches); -*/ +#endif } static void scoreShiftedLadderIons_( @@ -1578,6 +1580,35 @@ static void scoreXLIons_( return *longest; } + // note: this is much more efficient + size_t getLongestTagLength(const MSSpectrum& spec) const + { + // simple DP to detect longest tag + const size_t N = spec.size(); + if (N < 2) return 0; + std::vector mzs; + mzs.reserve(N); + for (auto const& p : spec) { mzs.push_back(p.getMZ()); } + std::vector max_tag(N, 0); // maximum tag length up to this peak + size_t longest_tag = 0; + for (size_t i = 0; i < N - 1; ++i) + { + for (size_t k = i + 1; k < N; ++k) + { + const double gap = mzs[k] - mzs[i]; + if (gap > max_gap_) { break; } + const char aa = getAAByMass_(gap); + if (aa == ' ') { continue; } // can't extend tag to k-th peak + if (max_tag[k] < max_tag[i] + 1) // check if we found a longer tag to k-th peak + { + ++max_tag[k]; // update longest tag to this peak + if (longest_tag < max_tag[k]) { longest_tag = max_tag[k]; } + } + } + } + return longest_tag; + } + private: float min_gap_; // will be set to smallest residue mass in ResidueDB float max_gap_; // will be set to highest residue mass in ResidueDB @@ -1851,7 +1882,9 @@ static void scoreXLIons_( spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].resize(1); spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = 0; #ifdef CALCULATE_LONGEST_TAG - spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = tagger.getLongestTag(spec).size(); + size_t longest_tag = tagger.getLongestTagLength(spec); + spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = longest_tag; + //spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = tagger.getLongestTag(spec).size(); // slow #endif spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].setName("longest_tag"); } From 3b7804672a90b1139b046d87751348de506ec72a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 31 Jul 2020 20:22:06 +0200 Subject: [PATCH 120/471] good invitro performance --- src/utils/OpenNuXL.cpp | 100 ++++++++++++++++++++++++++++++++++------- 1 file changed, 83 insertions(+), 17 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index dbf1737a856..61f45a94b12 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -561,7 +561,7 @@ class OpenNuXL : registerFlag_("RNPxl:only_xl", "Only search cross-links and ignore non-cross-linked peptides.", true); registerDoubleOption_("RNPxl:filter_small_peptide_mass", "", 600.0, "Filter precursor that can only correspond to non-crosslinks by mass.", false, true); - registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.05, "Tolerance used to determine marker ions (Da).", false, true); + registerDoubleOption_("RNPxl:marker_ions_tolerance", "", 0.03, "Tolerance used to determine marker ions (Da).", false, true); registerStringList_("filter", "", {"filter_pc_mass_error", "autotune", "idfilter"}, "Filtering steps applied to results.", false, true); setValidStrings_("filter", {"filter_pc_mass_error", "impute_decoy_medians", "filter_bad_partial_loss_scores", "autotune", "idfilter", "spectrumclusterfilter", "pcrecalibration"}); @@ -859,6 +859,7 @@ class OpenNuXL : } // match precusor ions z = 1..pc_charge + double pc_match_count(0); for (double pc_loss : {0.0, -18.010565, -17.026548} ) // normal, loss of water, loss of ammonia { for (Size z = 1; z <= pc_charge; ++z) @@ -876,6 +877,7 @@ class OpenNuXL : { const double intensity = exp_spectrum[index].getIntensity(); pc_MIC += intensity; + pc_match_count += 1.0; ++matches; peak_matched[index] = true; } @@ -884,6 +886,7 @@ class OpenNuXL : } } pc_MIC /= TIC; + pc_MIC += pc_match_count; // Morpheus score // shifted immonium ions @@ -1170,6 +1173,7 @@ class OpenNuXL : } // match (partially) shifted precusor ions z = 1..pc_charge + double pc_match_count(0); for (double pc_loss : {0.0, -18.010565, -17.026548} ) // normal, loss of water, loss of ammonia { const double peptide_mass = peptide_mass_without_NA + pc_loss; @@ -1191,6 +1195,7 @@ class OpenNuXL : { const double intensity = exp_spectrum[index].getIntensity(); plss_pc_MIC += intensity; + pc_match_count += 1.0; peak_matched[index] = true; } } @@ -1198,6 +1203,7 @@ class OpenNuXL : } } plss_pc_MIC /= TIC; + plss_pc_MIC += pc_match_count; // Morpheus score //////////////////////////////////////////////////////////////////////////////// // match shifted immonium ions @@ -1362,17 +1368,76 @@ score += ah.mass_error_p * 1.15386068 + isXL * 3.0 * ah.marker_ions_score + 3.0 * ah.total_MIC + ah.ladder_score; */ + + +/* return - 1.0 * ah.total_loss_score - + 0.1 * ah.partial_loss_score - + 0.1 * ah.mass_error_p + 47.29 * ah.total_loss_score + + 16.93 * ah.partial_loss_score + + 69.35 * ah.mass_error_p + - 72.84 * ah.err + - 75.65 * ah.pl_err + + 26.34 * ah.total_MIC + + 21.85 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) + + 39.64 * ah.ladder_score + + 60.15 * (ah.tag_shifted >= 1); +*/ +/* + return + 64.4 * ah.total_loss_score + + 21.3 * ah.partial_loss_score + + 98.97 * ah.mass_error_p + - 57.57 * ah.err + - 19.23 * ah.pl_err + + 0.23 * ah.total_MIC + + 16.47 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) + + 20.26 * ah.ladder_score + + 4.25 * (ah.tag_shifted >= 1); +*/ +/* + return + 0.90 * ah.total_loss_score + + 0.12 * ah.partial_loss_score + + 2.19 * ah.mass_error_p + - 54.60 * ah.err + - 71.06 * ah.pl_err + + 67.47 * ah.total_MIC + + 66.27 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) + + 11.45 * ah.ladder_score + + 28.09 * (ah.tag_shifted >= 1); +*/ + return 1.0 * ah.total_loss_score + + 0.5 * ah.partial_loss_score + + 1.0 * ah.mass_error_p - 0.1 * ah.err - 0.1 * ah.pl_err - + 0.1 * ah.pl_MIC + isXL * 0.1 * ah.marker_ions_score - + 0.1 * ah.total_MIC - + 0.1 * ah.ladder_score; + + 1.0 * ah.total_MIC + + isXL * (ah.pl_pc_MIC + ah.precursor_score) +// + 1.0 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) + + 0.1 * ah.ladder_score + + 1.0 * (ah.tag_shifted >= 1); + +/* + * [96.45142397 49.37352197 2.61098131 -1.21298196 -4.09934265 28.64381592 + * 53.84125899 41.37187898 7.66281392] + */ + + +/* + * good on IN VITRO: + 1.0 * ah.total_loss_score + + 0.5 * ah.partial_loss_score + + 1.0 * ah.mass_error_p + - 0.1 * ah.err + - 0.1 * ah.pl_err + + isXL * 0.1 * ah.marker_ions_score + + 1.0 * ah.total_MIC + + 1.0 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) + + 0.1 * ah.ladder_score + + 1.0 * (ah.tag_shifted >= 1); +*/ /* -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err + 52.2888 * ah.pl_err - 0.0105 * ah.modds @@ -1874,7 +1939,7 @@ static void scoreXLIons_( cout << " done!" << endl; cout << "Calculating longest mass tags..." << endl; - OpenNuXLTagger tagger(0.05, 3); + OpenNuXLTagger tagger(0.03, 3); for (auto & spec : exp) { if (spec.getMSLevel() != 2) continue; @@ -2019,7 +2084,7 @@ static void scoreXLIons_( // deisotope Deisotoper::deisotopeAndSingleCharge(spec, - 0.05, + 0.03, false, 1, 3, false, @@ -2053,7 +2118,7 @@ static void scoreXLIons_( NLargest nlargest_filter = NLargest(400); #ifdef DEBUG_OpenNuXL - BinnedSpectrum peak_density(MSSpectrum(), 0.05, false, 0, 0); + BinnedSpectrum peak_density(MSSpectrum(), 0.03, false, 0, 0); #endif #pragma omp parallel for @@ -2118,7 +2183,7 @@ static void scoreXLIons_( #endif #ifdef DEBUG_OpenNuXL - BinnedSpectrum bs(spec, 0.05, false, 0, 0); + BinnedSpectrum bs(spec, 0.03, false, 0, 0); bs.getBins().coeffs().cwiseMax(1); #pragma omp critical (peak_density_access) @@ -2138,7 +2203,7 @@ static void scoreXLIons_( ofstream dist_file; dist_file.open(getStringOption_("in") + ".fragment_dist.csv"); dist_file << "m/z\tfragments" << "\n"; - for (double mz = 0; mz < 2500.0; mz+=0.05) + for (double mz = 0; mz < 2500.0; mz+=0.03) { dist_file << mz << "\t" << peak_density.getBinIntensity(mz) << "\n"; } @@ -3562,7 +3627,7 @@ static void scoreXLIons_( im_MIC ); - const double tlss_total_MIC = tlss_MIC + im_MIC + pc_MIC; + const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); // early-out if super bad score if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { return; } @@ -4652,7 +4717,7 @@ static void scoreXLIons_( im_MIC ); - const double tlss_total_MIC = tlss_MIC + im_MIC + pc_MIC; + const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); if (badTotalLossScore(hyperScore, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; @@ -4829,7 +4894,7 @@ static void scoreXLIons_( im_MIC ); - const double tlss_total_MIC = tlss_MIC + im_MIC + pc_MIC; + const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); if (badTotalLossScore(hyperScore, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } vector intensity_xls(total_loss_template_z1_b_ions.size(), 0.0); @@ -4867,10 +4932,10 @@ static void scoreXLIons_( plss_pc_MIC, plss_im_MIC); - const double total_MIC = tlss_MIC + im_MIC + pc_MIC + plss_MIC + plss_pc_MIC + plss_im_MIC + marker_ions_sub_score; + const double total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)) + plss_MIC + (plss_pc_MIC - floor(plss_pc_MIC)) + plss_im_MIC + marker_ions_sub_score; // decreases number of hits (especially difficult cases - but also number of false discoveries) - if (filter_bad_partial_loss_scores && badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, plss_pc_MIC, marker_ions_sub_score)) + if (filter_bad_partial_loss_scores && badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, (plss_pc_MIC - floor(plss_pc_MIC)), marker_ions_sub_score)) { continue; } @@ -4931,6 +4996,7 @@ static void scoreXLIons_( // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, intensity_xls); + #ifdef FILTER_BAD_SCORES_ID_TAGS if (longest_tags.tag_XLed == 0) { continue; } #endif From 8404ab1d16d4350aa4aeebf7c7fc36634e07e178 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 12 Aug 2020 10:16:21 +0200 Subject: [PATCH 121/471] suffix / prefix aware tag calculation --- src/utils/OpenNuXL.cpp | 120 ++++++++++++++++++++++++++++++++++++++--- 1 file changed, 112 insertions(+), 8 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 61f45a94b12..1131cb93d78 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -3839,6 +3839,107 @@ static void scoreXLIons_( size_t tag_XLed = 0; // tag that contains the transition from unshifted to shifted }; + + XLTags getLongestABYLadderWithShift( + const vector& ab, + const vector& y, + const vector& ab_xl, + const vector& y_xl) + { + OPENMS_PRECONDITION(ab.size() == y.size(), "b and y ion arrays must have same size"); + OPENMS_PRECONDITION(ab_xl.size() == y_xl.size(), "cross-linked b and y ion arrays must have same size"); + + XLTags tags; + + const size_t n = ab.size(); + + // calculate longest consecutive unshifted / shifted sequence and longest sequence spanning unshifted + shifted residues + vector runAB(n, 0); + size_t run(0); + size_t max_ab_run(0); + for (int l = 0; l != n; ++l) + { + if (ab[l] == 0) { run = 0; continue; } + ++run; + runAB[l] = run; + if (run > max_ab_run) max_ab_run = run; + } + // runAB[i] now contains current run length e.g.: 000123400100 for prefix ions + + vector runY(n, 0); + run = 0; + size_t max_y_run(0); + for (int l = (int)n - 1; l >= 0; --l) + { + if (y[l] == 0) { run = 0; continue; } + ++run; + runY[l] = run; + if (run > max_y_run) max_y_run = run; + } + // runY[i] now contains current run length e.g.: 000432100100 for suffix ions + + tags.tag_unshifted = std::max(max_ab_run, max_y_run); + + const size_t n_xl = ab_xl.size(); + if (n_xl != 0) + { + OPENMS_PRECONDITION(n_xl == n, "xl and non-xl arrays need to have same size"); + + // for XL we calculate the runs in reverse order so we can later quickly calculate the maximum run + // through non-cross-linked and cross-linked ions + + vector runAB_XL(n_xl, 0); + run = 0; + size_t max_ab_shifted(0); + for (int x = (int)n_xl - 1; x >= 0; --x) // note the reverse order + { + if (ab_xl[x] == 0) { run = 0; continue; } + ++run; + runAB_XL[x] = run; + if (run > max_ab_shifted) max_ab_shifted = run; + } + // max_ab_shifted contains longest run of shifted ab ions + // runAB_XL[i] now contains the longest run in X starting at position i e.g.: 00003210000 for prefix ions + + vector runY_XL(n_xl, 0); + run = 0; + size_t max_y_shifted(0); + for (int x = 0; x != n_xl; ++x) + { + if (y_xl[x] == 0) { run = 0; continue; } + ++run; + runY_XL[x] = run; + if (run > max_y_shifted) max_y_shifted = run; + } + // runY_XL[i] now contains the longest run in X starting at position i e.g.: 00001230000 for suffix ions + + tags.tag_shifted = std::max(max_ab_shifted, max_y_shifted); + + size_t maximum_ab_tag_length(0); + + // calculate maximum tag that spans linear intensities and at least one XLed amino acid for prefix ions + for (Size i = 0; i < n_xl - 1; ++i) + { + if (runAB[i] == 0 || runAB_XL[i + 1] == 0) continue; // must have one cross-linked amino acid next to non-cross-linked amino acid + const size_t tag_length = runAB[i] + runAB_XL[i + 1]; // tag length if cross-link is introduced at amino acid i+1 + if (tag_length > maximum_ab_tag_length) maximum_ab_tag_length = tag_length; + } + + size_t maximum_y_tag_length(0); + + // same for suffix ions + for (Size i = 0; i < n_xl - 1; ++i) + { + if (runY_XL[i] == 0 || runY[i + 1] == 0) continue; // must have one cross-linked amino acid next to non-cross-linked amino acid + const size_t tag_length = runY_XL[i] + runY[i + 1]; // tag length with cross-linked part and non-cross-linked + if (tag_length > maximum_y_tag_length) maximum_y_tag_length = tag_length; + } + tags.tag_XLed = std::max(maximum_ab_tag_length, maximum_y_tag_length); + } + + return tags; + } + XLTags getLongestLadderWithShift(const vector& intL, const vector& intXL) { // calculate longest consecutive unshifted / shifted sequence and longest sequence spanning unshifted + shifted residues @@ -4753,7 +4854,10 @@ static void scoreXLIons_( ah.wTop50 = rankscores.wTop50; // do we have at least one ladder peak - const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, vector()); +// const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, vector()); + + const XLTags longest_tags = getLongestABYLadderWithShift(b_ions, y_ions, vector(), vector()); + #ifdef FILTER_BAD_SCORES_ID_TAGS if (longest_tags.tag_unshifted == 0) continue; #endif @@ -4899,10 +5003,9 @@ static void scoreXLIons_( vector intensity_xls(total_loss_template_z1_b_ions.size(), 0.0); -#ifdef DONT_ACCUMULATE_PARTIAL_ION_SCORES - std::fill(b_ions.begin(), b_ions.end(), 0); - std::fill(y_ions.begin(), y_ions.end(), 0); -#endif + vector b_xl_ions(b_ions.size(), 0.0); + vector y_xl_ions(b_ions.size(), 0.0); + float plss_MIC(0), plss_err(1.0), plss_Morph(0), @@ -4920,8 +5023,8 @@ static void scoreXLIons_( partial_loss_template_z1_yions, marker_ions_sub_score_spectrum_z1, intensity_xls, - b_ions, - y_ions, + b_xl_ions, + y_xl_ions, peak_matched, partial_loss_sub_score, marker_ions_sub_score, @@ -4995,7 +5098,8 @@ static void scoreXLIons_( // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one - const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, intensity_xls); +// const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, intensity_xls); + const XLTags longest_tags = getLongestABYLadderWithShift(b_ions, y_ions, b_xl_ions, y_xl_ions); #ifdef FILTER_BAD_SCORES_ID_TAGS if (longest_tags.tag_XLed == 0) { continue; } From bee5c044f376e50cbbf03a5246d62abf0e027f60 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 12 Aug 2020 12:41:06 +0200 Subject: [PATCH 122/471] 238/244 perc on in-vitro238/244 perc on in-vitro --- src/utils/OpenNuXL.cpp | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1131cb93d78..1316909e37d 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -134,6 +134,8 @@ using namespace boost::accumulators; //#define CALCULATE_NUCLEOTIDE_TAGS 1 #define DONT_ACCUMULATE_PARTIAL_ION_SCORES 1 +#define ANNOTATED_QUANTILES 1 + #ifdef ANNOTATED_QUANTILES typedef accumulator_set > quantile_accu_t; #endif @@ -1750,7 +1752,30 @@ static void scoreXLIons_( } }; + RankScores rankScores_(const MSSpectrum& spectrum, vector peak_matched) + { + RankScores r; + double matched = std::accumulate(peak_matched.begin(), peak_matched.end(), 0); + vector matched_ranks; + for (size_t i = 0; i != peak_matched.size(); ++i) + { + if (!peak_matched[i]) { continue; } + matched_ranks.push_back(spectrum.getIntegerDataArrays()[IA_RANK_INDEX][i]); + } + std::sort(matched_ranks.begin(), matched_ranks.end()); + // optimal ranking would be 0,1, ... , (number_of_matched_peaks - 1) + // calculate number of "insertions" of higher-intensity peaks compared to optimal ranking + size_t sum_rank_diff(matched_ranks[0]); + for (size_t i = 1; i != matched_ranks.size(); ++i) + { + sum_rank_diff += matched_ranks[i] - matched_ranks[0] - 1; + } + + r.wTop50 = log10(1.0 + sum_rank_diff); + return r; + } +/* RankScores rankScores_(const MSSpectrum& spectrum, vector peak_matched) { double matched = std::accumulate(peak_matched.begin(), peak_matched.end(), 0); @@ -1781,6 +1806,7 @@ static void scoreXLIons_( r.rp = exp(r.rp - 1.0 / matched * lgamma(matched+1)); // = rp / lowest possible rp given number of matches return r; } +*/ #ifdef FILTER_AMBIGIOUS_PEAKS static map mass2high_frequency_; From 4685b44de5773cff328490c03f735bd714297db6 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 13 Aug 2020 16:43:15 +0200 Subject: [PATCH 123/471] minor changes --- src/utils/OpenNuXL.cpp | 30 ++++++++++++++++++++++++++---- 1 file changed, 26 insertions(+), 4 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1316909e37d..55cb895d41a 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -633,7 +633,7 @@ class OpenNuXL : // Nd/w (number of peaks in spectrum * fragment mass tolerance in Da / MS/MS mass range in Da - see phoshoRS) //const double p = peaks_in_spectrum * fragment_mass_tolerance_Da / mass_range_Da; - const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see ThresholdMower) + const double p = 20.0 / 100.0; // level 20.0 / mz 100.0 (see WindowMower) const double pscore = boost::math::ibeta(matched_size + 1, N - matched_size, p); if (pscore <= std::numeric_limits::min()) return -log10(std::numeric_limits::min()); const double minusLog10p1pscore = -log10(pscore); @@ -1041,6 +1041,9 @@ class OpenNuXL : double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 + size_t comparisons(0); + size_t matches(0); + // maximum charge considered const unsigned int max_z = std::min(2U, static_cast(pc_charge - 1)); @@ -1082,8 +1085,10 @@ class OpenNuXL : dot_product += intensity; b_ions[i] += intensity; peak_matched[index] = true; + matches++; } } + ++comparisons; } } } @@ -1124,8 +1129,10 @@ class OpenNuXL : dot_product += intensity; y_ions[N-1 - i] += intensity; peak_matched[index] = true; + matches++; } } + ++comparisons; } } } @@ -1199,8 +1206,10 @@ class OpenNuXL : plss_pc_MIC += intensity; pc_match_count += 1.0; peak_matched[index] = true; + matches++; } } + ++comparisons; } } } @@ -1222,8 +1231,10 @@ class OpenNuXL : { score += exp_spectrum[index].getIntensity(); peak_matched[index] = true; + matches++; } } + ++comparisons; }; static const double imY = EmpiricalFormula("C8H10NO").getMonoWeight(); @@ -1299,12 +1310,22 @@ class OpenNuXL : const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000; +#ifdef MODDS_ON_ABY_IONS_ONLY plss_modds = matchOddsScore_( partial_loss_template_z1_b_ions.size() + partial_loss_template_z1_y_ions.size(), fragment_mass_tolerance_Da, exp_spectrum.size(), exp_spectrum.back().getMZ(), (int)plss_Morph); +#else + plss_modds = matchOddsScore_( + comparisons, + fragment_mass_tolerance_Da, + exp_spectrum.size(), + exp_spectrum.back().getMZ(), + matches); +#endif + } /* @@ -5068,6 +5089,7 @@ static void scoreXLIons_( { continue; } + const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); @@ -5337,16 +5359,16 @@ static void scoreXLIons_( for (Size scan_index = 0; scan_index != peptide_ids.size(); ++scan_index) { PeptideIdentification& pi = peptide_ids[scan_index]; - cout << "score\tpeptides\tXLs\ttype" << endl; +// cout << "score\tpeptides\tXLs\ttype" << endl; for (auto & ph : pi.getHits()) { if (ph.getMetaValue("NuXL:isXL") == "1") { - ph.setMetaValue("NuXL:total_HS", (double)ph.getMetaValue("NuXL:total_HS") / p_square_quantile(annotated_peptides_quantiles_XLs[scan_index])); + ph.setMetaValue("NuXL:total_HS", (double)ph.getMetaValue("NuXL:total_HS") / (1.0 + p_square_quantile(annotated_peptides_quantiles_XLs[scan_index]))); } else { - ph.setMetaValue("NuXL:total_HS", (double)ph.getMetaValue("NuXL:total_HS") / p_square_quantile(annotated_peptides_quantiles_peptides[scan_index])); + ph.setMetaValue("NuXL:total_HS", (double)ph.getMetaValue("NuXL:total_HS") / (1.0 + p_square_quantile(annotated_peptides_quantiles_peptides[scan_index]))); } } } From 76e50b84d33e6b409fa7caa0362e862829a89ee6 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 24 Aug 2020 20:08:10 +0200 Subject: [PATCH 124/471] bump THIRDPARTY --- THIRDPARTY | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/THIRDPARTY b/THIRDPARTY index d8eaed71ed0..2c4710213b2 160000 --- a/THIRDPARTY +++ b/THIRDPARTY @@ -1 +1 @@ -Subproject commit d8eaed71ed038a3660c87282025fb3f39054d978 +Subproject commit 2c4710213b229fb886c56ff9a39ec6c52e308918 From a9aef8b7bd6ec30ee13cda9cf278e0af4ed2e160 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 26 Aug 2020 16:37:29 +0200 Subject: [PATCH 125/471] C/N-term ammonia loss in TSG and fraction of peaks matched and masking of neutral loss peaks --- .../CHEMISTRY/TheoreticalSpectrumGenerator.h | 1 + .../TheoreticalSpectrumGenerator.cpp | 36 ++++ src/utils/OpenNuXL.cpp | 204 ++++++++++++++++-- 3 files changed, 221 insertions(+), 20 deletions(-) diff --git a/src/openms/include/OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h b/src/openms/include/OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h index 453969f9a11..29f8e06b5a2 100644 --- a/src/openms/include/OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h +++ b/src/openms/include/OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h @@ -127,6 +127,7 @@ namespace OpenMS bool add_z_ions_; bool add_first_prefix_ion_; bool add_losses_; + bool add_term_losses_; bool add_metainfo_; bool add_isotopes_; int isotope_model_; diff --git a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp index c2516228ef8..c2a0858e2e8 100644 --- a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp +++ b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp @@ -64,6 +64,9 @@ namespace OpenMS defaults_.setValue("add_losses", "false", "Adds common losses to those ion expect to have them, only water and ammonia loss is considered"); defaults_.setValidStrings("add_losses", ListUtils::create("true,false")); + defaults_.setValue("add_term_losses", "false", "Adds common N- and C-term losses (only if add_losses=true and isotope_model=none), only water and ammonia loss is considered."); + defaults_.setValidStrings("add_term_losses", ListUtils::create("true,false")); + defaults_.setValue("sort_by_position", "true", "Sort output by position"); defaults_.setValidStrings("sort_by_position", ListUtils::create("true,false")); @@ -521,6 +524,25 @@ namespace OpenMS } } } + if (add_term_losses_) + { + { + auto formula = EmpiricalFormula("H2O"); + String& loss_name = formula_str_cache[formula]; + if (loss_name.empty()) + { + loss_name = formula.toString(); + } + } + { + auto formula = EmpiricalFormula("NH3"); + String& loss_name = formula_str_cache[formula]; + if (loss_name.empty()) + { + loss_name = formula.toString(); + } + } + } } if (res_type == Residue::AIon || res_type == Residue::BIon || res_type == Residue::CIon) @@ -576,6 +598,11 @@ namespace OpenMS mono_weight = initial_mono_weight; if (add_losses_) { + if (add_term_losses_) + { + fx_losses.insert(EmpiricalFormula("H2O")); // HCD water loss at N-term + } + for (i = Size(!add_first_prefix_ion_); i < peptide.size() - 1; ++i) { mono_weight += peptide[i].getMonoWeight(Residue::Internal); // standard internal residue including named modifications: c @@ -592,6 +619,7 @@ namespace OpenMS { for (const auto& formula : peptide[i].getLossFormulas()) fx_losses.insert(formula); } + addLossesFaster_(spectrum, mono_weight + ion_offset, fx_losses, i + 1, ion_names, charges, formula_str_cache, intensity * rel_loss_intensity_, res_type, add_metainfo_, charge); @@ -665,6 +693,12 @@ namespace OpenMS if (add_losses_) { + if (add_term_losses_) + { + fx_losses.insert(EmpiricalFormula("H2O")); // HCD water and ammonia loss at C-term + fx_losses.insert(EmpiricalFormula("NH3")); + } + mono_weight = initial_mono_weight; for (Size i = peptide.size() - 1; i > 0; --i) { @@ -682,6 +716,7 @@ namespace OpenMS { for (const auto& formula : peptide[i].getLossFormulas()) fx_losses.insert(formula); } + addLossesFaster_(spectrum, mono_weight + ion_offset, fx_losses, peptide.size() - i, ion_names, charges, formula_str_cache, intensity * rel_loss_intensity_, res_type, add_metainfo_, charge); @@ -896,6 +931,7 @@ namespace OpenMS add_z_ions_ = param_.getValue("add_z_ions").toBool(); add_first_prefix_ion_ = param_.getValue("add_first_prefix_ion").toBool(); add_losses_ = param_.getValue("add_losses").toBool(); + add_term_losses_ = param_.getValue("add_term_losses").toBool(); add_metainfo_ = param_.getValue("add_metainfo").toBool(); add_isotopes_ = param_.getValue("isotope_model") != "none"; if (param_.getValue("isotope_model") == "coarse") isotope_model_ = 1; diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 55cb895d41a..31424639867 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -134,10 +134,54 @@ using namespace boost::accumulators; //#define CALCULATE_NUCLEOTIDE_TAGS 1 #define DONT_ACCUMULATE_PARTIAL_ION_SCORES 1 +#define CONSIDER_AA_LOSSES 1 + #define ANNOTATED_QUANTILES 1 #ifdef ANNOTATED_QUANTILES typedef accumulator_set > quantile_accu_t; + +#include + +typedef accumulator_set > accumulator_t_quadratic; + +struct SpectrumLevelScoreQuantiles +{ + SpectrumLevelScoreQuantiles(): + acc_(extended_p_square_probabilities = std::vector{ 0.0, 0.25, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99, 1.00 }) + { + } + void insert(double v) { acc_(v); } + + double quantileOfValue(double v) + { + double l = 0.0; + double h = 1.0; + double mid = l + (h - l) / 2.0; // we start with the median (0.5) + double p_value = quantile(acc_, quantile_probability = mid); // value of quantile p + + size_t iter(0); + while (fabs(p_value - v) > 0.01 && iter < 100) + { + mid = l + (h - l) / 2.0; + p_value = quantile(acc_, quantile_probability = mid); // value of quantile p (e.g., 1234.56) + if (p_value > v) // if the current quantile value (e.g., of the median) has a value larger than our value of interest + { + h = mid; // then we need to search in the lower quantile range + } + else + { + l = mid; + } + ++iter; + } + return l; + } + private: + accumulator_t_quadratic acc_; +}; + + #endif using namespace OpenMS; @@ -374,7 +418,7 @@ class AnnotatedHit size_t tag_shifted = 0; size_t tag_XLed = 0; // tag that contains the transition from unshifted to shifted - double rank_product = 0; + double explained_peak_fraction = 0; double wTop50 = 0; static bool hasBetterScore(const AnnotatedHit& a, const AnnotatedHit& b) @@ -812,6 +856,57 @@ class OpenNuXL : } } +#ifdef CONSIDER_AA_LOSSES + // block peaks matching to AA related neutral losses so they don't get matched to NA shifts + // b-H2O + for (double diff2b : { -18.010565 } ) + { + for (Size z = 1; z <= max_z; ++z) + { + for (Size i = 0; i < total_loss_template_z1_b_ions.size(); ++i) + { + const double theo_mz = (total_loss_template_z1_b_ions[i] + diff2b + + (z-1) * Constants::PROTON_MASS_U) / z; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + Size index = exp_spectrum.findNearest(theo_mz); + const double exp_mz = exp_spectrum[index].getMZ(); + const Size exp_z = exp_charges[index]; + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + if (!peak_matched[index]) + { + peak_matched[index] = true; + } + } + } + } + } + + // y-H2O and y-NH3 + for (double diff2b : { -18.010565, -17.026549 } ) + { + for (Size z = 1; z <= max_z; ++z) + { + for (Size i = 0; i < total_loss_template_z1_y_ions.size(); ++i) + { + const double theo_mz = (total_loss_template_z1_y_ions[i] + diff2b + + (z-1) * Constants::PROTON_MASS_U) / z; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + Size index = exp_spectrum.findNearest(theo_mz); + const double exp_mz = exp_spectrum[index].getMZ(); + const Size exp_z = exp_charges[index]; + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + if (!peak_matched[index]) + { + peak_matched[index] = true; + } + } + } + } + } +#endif + // determine b+a and y-ion count UInt y_ion_count(0), b_ion_count(0); double b_sum(0.0); @@ -1137,6 +1232,72 @@ class OpenNuXL : } } + +#ifdef CONSIDER_AA_LOSSES + // block peaks matching to AA related neutral losses so they don't get matched to NA shifts + // b-H2O + for (double diff2b : { -18.010565 } ) + { + for (Size z = 1; z <= max_z; ++z) + { + for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) + { + for (Size i = 0; i < partial_loss_template_z1_b_ions.size(); ++i) + { + const double theo_mz = (partial_loss_template_z1_b_ions[i] + fa.mass + diff2b + + (z-1) * Constants::PROTON_MASS_U) / z; + + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + Size index = exp_spectrum.findNearest(theo_mz); + const double exp_mz = exp_spectrum[index].getMZ(); + const Size exp_z = exp_charges[index]; + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + if (!peak_matched[index]) + { + peak_matched[index] = true; + } + } + } + } + } + } + + // match y-ions + // y-H2O and y-NH3 + for (double diff2b : { -18.010565, -17.026549 } ) + for (Size z = 1; z <= max_z; ++z) + { + for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) + { + for (Size i = 1; i < partial_loss_template_z1_y_ions.size(); ++i) // Note that we start at (i=1 -> y2) as trypsin would otherwise not cut at cross-linking site + { + const double theo_mz = (partial_loss_template_z1_y_ions[i] + fa.mass + diff2b + + (z-1) * Constants::PROTON_MASS_U) / z; + + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + Size index = exp_spectrum.findNearest(theo_mz); + const double exp_mz = exp_spectrum[index].getMZ(); + const Size exp_z = exp_charges[index]; + + if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + { + if (!peak_matched[index]) + { + peak_matched[index] = true; + } + } + } + } + } +#endif + + + + + + + UInt y_ion_count(0), b_ion_count(0); double b_sum(0.0); for (Size i = 0; i != b_ions.size(); ++i) @@ -1743,7 +1904,7 @@ static void scoreXLIons_( struct RankScores { - double rp = 0; // normalized intensity rank product + double explained_peak_fraction = 0; double wTop50 = 0; }; @@ -1776,7 +1937,8 @@ static void scoreXLIons_( RankScores rankScores_(const MSSpectrum& spectrum, vector peak_matched) { RankScores r; - double matched = std::accumulate(peak_matched.begin(), peak_matched.end(), 0); + if (spectrum.empty()) return r; + const double matched = std::accumulate(peak_matched.begin(), peak_matched.end(), 0); vector matched_ranks; for (size_t i = 0; i != peak_matched.size(); ++i) { @@ -1794,6 +1956,7 @@ static void scoreXLIons_( } r.wTop50 = log10(1.0 + sum_rank_diff); + r.explained_peak_fraction = matched / (double)spectrum.size(); return r; } /* @@ -2565,16 +2728,17 @@ static void scoreXLIons_( // but as we also add the abundant immonium ions for charge 1 and precursor ions for all charges to get a more complete annotation // (these have previously not been used in the scoring of the total loss spectrum) PeakSpectrum total_loss_spectrum; - - TheoreticalSpectrumGenerator tmp_generator; - Param new_param(partial_loss_spectrum_generator.getParameters()); - new_param.setValue("add_all_precursor_charges", "true"); - new_param.setValue("add_abundant_immonium_ions", "true"); - new_param.setValue("add_losses", "true"); - new_param.setValue("add_a_ions", "true"); - - tmp_generator.setParameters(new_param); - tmp_generator.getSpectrum(total_loss_spectrum, fixed_and_variable_modified_peptide, 1, precursor_charge); + { + TheoreticalSpectrumGenerator tmp_generator; + Param new_param(partial_loss_spectrum_generator.getParameters()); + new_param.setValue("add_all_precursor_charges", "true"); + new_param.setValue("add_abundant_immonium_ions", "true"); + new_param.setValue("add_losses", "true"); + new_param.setValue("add_term_losses", "true"); + new_param.setValue("add_a_ions", "true"); + tmp_generator.setParameters(new_param); + tmp_generator.getSpectrum(total_loss_spectrum, fixed_and_variable_modified_peptide, 1, precursor_charge); + } // add special immonium ions RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( @@ -3316,7 +3480,7 @@ static void scoreXLIons_( const double id2maxtag = maxtag == 0 ? 0 : (ah.ladder_score * s.size()) / (double)maxtag; ph.setMetaValue("NuXL:aminoacid_id_to_max_tag_ratio", id2maxtag); ph.setMetaValue("nr_candidates", nr_candidates[scan_index]); - ph.setMetaValue("NuXL:rank_product", ah.rank_product); + ph.setMetaValue("NuXL:explained_peak_fraction", ah.explained_peak_fraction); ph.setMetaValue("NuXL:wTop50", ah.wTop50); ph.setPeakAnnotations(ah.fragment_annotations); @@ -3355,8 +3519,8 @@ static void scoreXLIons_( const map& purities, const vector& nr_candidates) { - assert(annotated_XL_hits.size() == annotated_peptide_hits.size()); - SignedSize hit_count = static_cast(annotated_XL_hits.size()); + assert(annotated_XL_hits.size() == annotated_peptide_hits.size()); + SignedSize hit_count = static_cast(annotated_XL_hits.size()); for (SignedSize scan_index = 0; scan_index < hit_count; ++scan_index) { @@ -3477,7 +3641,7 @@ static void scoreXLIons_( << "NuXL:aminoacid_max_tag" << "NuXL:aminoacid_id_to_max_tag_ratio" << "nr_candidates" - << "NuXL:rank_product" + << "NuXL:explained_peak_fraction" << "NuXL:wTop50"; feature_set @@ -4897,7 +5061,7 @@ static void scoreXLIons_( } RankScores rankscores = rankScores_(exp_spectrum, peak_matched); - ah.rank_product = rankscores.rp; + ah.explained_peak_fraction = rankscores.explained_peak_fraction; ah.wTop50 = rankscores.wTop50; // do we have at least one ladder peak @@ -5141,7 +5305,7 @@ static void scoreXLIons_( } RankScores rankscores = rankScores_(exp_spectrum, peak_matched); - ah.rank_product = rankscores.rp; + ah.explained_peak_fraction = rankscores.explained_peak_fraction; ah.wTop50 = rankscores.wTop50; @@ -5674,7 +5838,7 @@ static void scoreXLIons_( << "NuXL:tag_XLed" << "NuXL:tag_unshifted" << "NuXL:tag_shifted" - << "NuXL:rank_product" + << "NuXL:explained_peak_fraction" << "NuXL:isXL" << "NuXL:wTop50"; From 5da62f5a822ad12e940ae3d3581dda6dd67416eb Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 28 Aug 2020 14:35:54 +0200 Subject: [PATCH 126/471] [FEATURE] annotate internal ions --- .../CHEMISTRY/TheoreticalSpectrumGenerator.h | 13 +- .../TheoreticalSpectrumGenerator.cpp | 168 +++++++++++++++++- src/utils/OpenNuXL.cpp | 53 +++++- 3 files changed, 221 insertions(+), 13 deletions(-) diff --git a/src/openms/include/OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h b/src/openms/include/OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h index 29f8e06b5a2..af8f21bda06 100644 --- a/src/openms/include/OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h +++ b/src/openms/include/OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h @@ -117,8 +117,16 @@ namespace OpenMS void addLosses_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, double intensity, const Residue::ResidueType res_type, int charge) const; /// helper to add full neutral loss ladders (for single peaks), also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true - void addLossesFaster_(PeakSpectrum& spectrum, double mz, const std::set& f_losses, int ion_ordinal, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, const std::map& formula_str_cache, double intensity, const Residue::ResidueType res_type, bool add_metainfo, int charge) const; - + void addLossesFaster_(PeakSpectrum& spectrum, double mz, const std::set& f_losses, int ion_ordinal, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, const std::map& formula_str_cache, double intensity, const String& annotation_prefix_string, bool add_metainfo, int charge) const; + + void addInternalFragmentPeaks_(PeakSpectrum& spectrum, + const AASequence& peptide, + DataArrays::StringDataArray& ion_names, + DataArrays::IntegerDataArray& charges, + MSSpectrum::Chunks& chunks, + const Residue::ResidueType res_type, + Int charge) const; + bool add_b_ions_; bool add_y_ions_; bool add_a_ions_; @@ -130,6 +138,7 @@ namespace OpenMS bool add_term_losses_; bool add_metainfo_; bool add_isotopes_; + bool add_internal_fragments_; int isotope_model_; bool add_precursor_peaks_; bool add_all_precursor_charges_ ; diff --git a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp index c2a0858e2e8..5333da37a15 100644 --- a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp +++ b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp @@ -67,6 +67,9 @@ namespace OpenMS defaults_.setValue("add_term_losses", "false", "Adds common N- and C-term losses (only if add_losses=true and isotope_model=none), only water and ammonia loss is considered."); defaults_.setValidStrings("add_term_losses", ListUtils::create("true,false")); + defaults_.setValue("add_internal_fragments", "false", "Add b and a type fragments from internal cleavage events."); + defaults_.setValidStrings("add_internal_fragments", ListUtils::create("true,false")); + defaults_.setValue("sort_by_position", "true", "Sort output by position"); defaults_.setValidStrings("sort_by_position", ListUtils::create("true,false")); @@ -179,6 +182,15 @@ namespace OpenMS if (add_z_ions_) addPeaks_(spectrum, peptide, *ion_names, *charges, chunks, Residue::ZIon, z); } + if (add_internal_fragments_) + { + for (Int z = min_charge; z <= max_charge; ++z) + { + addInternalFragmentPeaks_(spectrum, peptide, *ion_names, *charges, chunks, Residue::BIon, z); + addInternalFragmentPeaks_(spectrum, peptide, *ion_names, *charges, chunks, Residue::AIon, z); + } + } + if (add_precursor_peaks_) { if (add_all_precursor_charges_) @@ -362,12 +374,11 @@ namespace OpenMS DataArrays::IntegerDataArray& charges, const std::map& formula_str_cache, double intensity, - const Residue::ResidueType res_type, + const String& annotation_prefix_string, bool add_metainfo, int charge) const { - const String residue_str(Residue::residueTypeToIonLetter(res_type)); - const String ion_ordinal_str(String(ion_ordinal) + "-"); + const String ion_ordinal_str = ion_ordinal < 0 ? "-" : String(ion_ordinal) + "-"; // only add ion number for non-negative values for (auto& formula : f_losses) { @@ -377,7 +388,7 @@ namespace OpenMS { const String& loss_name = formula_str_cache.at(formula); // note: important to construct a string from char. If omitted it will perform pointer arithmetics on the "-" string literal - ion_names.emplace_back(residue_str); + ion_names.emplace_back(annotation_prefix_string); //note: size of Residue::residueTypeToIonLetter(res_type) : 1; ion_names.back().reserve(1 + ion_ordinal_str.size() + loss_name.size()); ((ion_names.back() += ion_ordinal_str) += loss_name); @@ -474,6 +485,148 @@ namespace OpenMS } + void TheoreticalSpectrumGenerator::addInternalFragmentPeaks_(PeakSpectrum& spectrum, + const AASequence& peptide, + DataArrays::StringDataArray& ion_names, + DataArrays::IntegerDataArray& charges, + MSSpectrum::Chunks& chunks, + const Residue::ResidueType res_type, + Int charge) const + { + static double stat_a = Residue::getInternalToAIon().getMonoWeight(); + static double stat_b = Residue::getInternalToBIon().getMonoWeight(); + + int f = 1 + int(add_isotopes_) + int(add_losses_); // TODO: calculate number of internal fragments + spectrum.reserve(spectrum.size() + f * peptide.size()); + + // precompute formula_str_cache + std::map formula_str_cache; + if (add_losses_) + { + for (auto& p : peptide) + { + for (auto& formula : p.getLossFormulas()) + { + String& loss_name = formula_str_cache[formula]; + if (loss_name.empty()) + { + loss_name = formula.toString(); + } + } + } + if (add_term_losses_) + { + { + auto formula = EmpiricalFormula("H2O"); + String& loss_name = formula_str_cache[formula]; + if (loss_name.empty()) + { + loss_name = formula.toString(); + } + } + { + auto formula = EmpiricalFormula("NH3"); + String& loss_name = formula_str_cache[formula]; + if (loss_name.empty()) + { + loss_name = formula.toString(); + } + } + } + } + + for (Size l = 1; l < peptide.size() - 1 - 2; ++l) // start at a2/b2, stop at n-1 a/b ion with min length of 2 + { + double intensity(1); + + // support for b and a type internal ions, TODO: own intensity for these type of ions? + switch (res_type) + { + case Residue::AIon: intensity = a_intensity_; break; + case Residue::BIon: intensity = b_intensity_; break; + default: break; + } + + double mono_weight(Constants::PROTON_MASS_U * charge); + + std::set fx_losses; + + double initial_mono_weight(mono_weight); + + String ion_name; + for (size_t i = l; i < peptide.size() - 1; ++i) + { + if (i-l >= 10) break; // unlikely to observe longer internal fragments + + mono_weight += peptide[i].getMonoWeight(Residue::Internal); // standard internal residue including named modifications: c + ion_name += peptide[i].getOneLetterCode(); + + if (i==l) continue; // don't generate peak for single AA + + double pos(mono_weight); + double ion_offset = 0; + switch (res_type) + { + case Residue::AIon: ion_offset = stat_a; break; + case Residue::BIon: ion_offset = stat_b; break; + default: break; + } + pos = (pos + ion_offset) / charge; + + spectrum.emplace_back(pos, intensity); + if (add_metainfo_) + { + if (res_type == Residue::AIon) + { + ion_names.emplace_back(ion_name + "-CO"); + } + else // Residue::BIon + { + ion_names.emplace_back(ion_name); + } + charges.push_back(charge); + } + } + chunks.add(true); + + if (add_losses_) + { + mono_weight = initial_mono_weight; + String ion_name; + for (size_t i = l; i < peptide.size() - 1; ++i) + { + if (i-l >= 10) break; // unlikely to observe longer internal fragments + + mono_weight += peptide[i].getMonoWeight(Residue::Internal); // standard internal residue including named modifications: c + ion_name += peptide[i].getOneLetterCode(); + + if (i==l) continue; // don't generate peak for single AA + + double ion_offset = 0; + switch (res_type) + { + case Residue::AIon: ion_offset = stat_a; break; + case Residue::BIon: ion_offset = stat_b; break; + default: break; + } + if (peptide[i].hasNeutralLoss()) + { + for (const auto& formula : peptide[i].getLossFormulas()) fx_losses.insert(formula); + } + + const String annotation_prefix_string = (res_type == Residue::AIon) ? ion_name + "-CO" : ion_name; // add string indicating a-ion + + addLossesFaster_(spectrum, mono_weight + ion_offset, fx_losses, + -1, ion_names, charges, formula_str_cache, intensity * rel_loss_intensity_, // -1 = don't add ion number for internal ions + annotation_prefix_string, add_metainfo_, charge); + chunks.add(false); // unfortunately, the losses are not always inserted in sorted order + } + } + } + + } + + void TheoreticalSpectrumGenerator::addPeaks_(PeakSpectrum& spectrum, const AASequence& peptide, DataArrays::StringDataArray& ion_names, @@ -598,6 +751,7 @@ namespace OpenMS mono_weight = initial_mono_weight; if (add_losses_) { + const String annotation_prefix_string(Residue::residueTypeToIonLetter(res_type)); if (add_term_losses_) { fx_losses.insert(EmpiricalFormula("H2O")); // HCD water loss at N-term @@ -622,7 +776,7 @@ namespace OpenMS addLossesFaster_(spectrum, mono_weight + ion_offset, fx_losses, i + 1, ion_names, charges, formula_str_cache, intensity * rel_loss_intensity_, - res_type, add_metainfo_, charge); + annotation_prefix_string, add_metainfo_, charge); chunks.add(false); // unfortunately, the losses are not always inserted in sorted order } } @@ -693,6 +847,7 @@ namespace OpenMS if (add_losses_) { + const String annotation_prefix_string(Residue::residueTypeToIonLetter(res_type)); if (add_term_losses_) { fx_losses.insert(EmpiricalFormula("H2O")); // HCD water and ammonia loss at C-term @@ -719,7 +874,7 @@ namespace OpenMS addLossesFaster_(spectrum, mono_weight + ion_offset, fx_losses, peptide.size() - i, ion_names, charges, formula_str_cache, intensity * rel_loss_intensity_, - res_type, add_metainfo_, charge); + annotation_prefix_string, add_metainfo_, charge); chunks.add(false); // losses are not always added in sorted order } } @@ -934,6 +1089,7 @@ namespace OpenMS add_term_losses_ = param_.getValue("add_term_losses").toBool(); add_metainfo_ = param_.getValue("add_metainfo").toBool(); add_isotopes_ = param_.getValue("isotope_model") != "none"; + add_internal_fragments_ = param_.getValue("add_internal_fragments").toBool(); if (param_.getValue("isotope_model") == "coarse") isotope_model_ = 1; else if (param_.getValue("isotope_model") == "fine") isotope_model_ = 2; sort_by_position_ = param_.getValue("sort_by_position").toBool(); diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 31424639867..790e5595f22 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -125,7 +125,7 @@ using namespace boost::accumulators; //#define OPENNUXL_SEPARATE_FEATURES 1 //#define DANGEROUS_FEAUTURES increases FDR on entrappment dataset //#define FILTER_BAD_SCORES_ID_TAGS filter out some good hits -//#define FILTER_AMBIGIOUS_PEAKS +//#define FILTER_AMBIGIOUS_PEAKS so far only worse results //#define FILTER_NO_ARBITRARY_TAG_PRESENT #define CALCULATE_LONGEST_TAG //#define MODDS_ON_ABY_IONS_ONLY @@ -148,7 +148,7 @@ typedef accumulator_set{ 0.0, 0.25, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99, 1.00 }) + acc_(extended_p_square_probabilities = std::vector{ 0.0, 0.25, 0.5, 0.75, 0.9, 0.95, 0.99, 0.999, 0.9999, 0.99999, 1.00 }) { } void insert(double v) { acc_(v); } @@ -181,7 +181,6 @@ struct SpectrumLevelScoreQuantiles accumulator_t_quadratic acc_; }; - #endif using namespace OpenMS; @@ -857,7 +856,7 @@ class OpenNuXL : } #ifdef CONSIDER_AA_LOSSES - // block peaks matching to AA related neutral losses so they don't get matched to NA shifts + // block peaks matching to AA related neutral losses so they get counted for explained peak fraction calculation // b-H2O for (double diff2b : { -18.010565 } ) { @@ -2657,6 +2656,7 @@ static void scoreXLIons_( param.setValue("add_x_ions", "false"); param.setValue("add_y_ions", "true"); param.setValue("add_z_ions", "false"); + param.setValue("add_internal_fragments", "true"); partial_loss_spectrum_generator.setParameters(param); #ifdef _OPENMP #pragma omp parallel for @@ -2736,6 +2736,7 @@ static void scoreXLIons_( new_param.setValue("add_losses", "true"); new_param.setValue("add_term_losses", "true"); new_param.setValue("add_a_ions", "true"); + new_param.setValue("add_internal_fragments", "true"); tmp_generator.setParameters(new_param); tmp_generator.getSpectrum(total_loss_spectrum, fixed_and_variable_modified_peptide, 1, precursor_charge); } @@ -2930,6 +2931,16 @@ static void scoreXLIons_( annotated_immonium_ions.push_back(fa); peak_is_annotated.insert(aligned.second); } + else if (isupper(ion_name[0])) // internal ions + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + annotated_immonium_ions.push_back(fa); //TODO: add to annotated_internal_fragment_ions or rename vector + peak_is_annotated.insert(aligned.second); + } } // generate fragment annotation strings for unshifted ions @@ -3079,9 +3090,20 @@ static void scoreXLIons_( fa.mz = fragment_mz; fa.intensity = fragment_intensity; fa.charge = charge; - fa.annotation = ion_name; + fa.annotation = ion_name; annotated_precursor_ions.push_back(fa); } + else if (isupper(ion_name[0])) // shifted internal ions + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + String with_plus = ion_name; + with_plus.substitute(' ', '+'); + fa.annotation = with_plus; // turn "PEPT U-H2O" into "PEPT+U-H20" + shifted_immonium_ions.push_back(fa); //TODO: add to shfited_internal_fragment_ions or rename vector + } } // track shifts in n- and c-term ladders (in AAs coordinates) @@ -3642,6 +3664,8 @@ static void scoreXLIons_( << "NuXL:aminoacid_id_to_max_tag_ratio" << "nr_candidates" << "NuXL:explained_peak_fraction" + << "NuXL:QQ_TIC" + << "NuXL:QQ_EXPLAINED_FRACTION" << "NuXL:wTop50"; feature_set @@ -4790,6 +4814,9 @@ static void scoreXLIons_( #ifdef ANNOTATED_QUANTILES vector annotated_peptides_quantiles_peptides(spectra.size(), quantile_accu_t(quantile_probability = 0.95)); vector annotated_peptides_quantiles_XLs(spectra.size(), quantile_accu_t(quantile_probability = 0.95)); + + vector QQ_TIC(spectra.size(), SpectrumLevelScoreQuantiles() ); + vector QQ_EXPLAINED_FRACTION(spectra.size(), SpectrumLevelScoreQuantiles() ); #endif // load fasta file @@ -5090,6 +5117,9 @@ static void scoreXLIons_( { #ifdef ANNOTATED_QUANTILES annotated_peptides_quantiles_peptides[scan_index](ah.total_loss_score); + + QQ_TIC[scan_index].insert(ah.total_MIC); + QQ_EXPLAINED_FRACTION[scan_index].insert(ah.explained_peak_fraction); #endif annotated_peptides[scan_index].emplace_back(move(ah)); @@ -5334,6 +5364,9 @@ static void scoreXLIons_( { #ifdef ANNOTATED_QUANTILES annotated_peptides_quantiles_XLs[scan_index](ah.total_loss_score + ah.partial_loss_score); + + QQ_TIC[scan_index].insert(ah.total_MIC); + QQ_EXPLAINED_FRACTION[scan_index].insert(ah.explained_peak_fraction); #endif annotated_XLs[scan_index].emplace_back(move(ah)); @@ -5535,6 +5568,16 @@ static void scoreXLIons_( ph.setMetaValue("NuXL:total_HS", (double)ph.getMetaValue("NuXL:total_HS") / (1.0 + p_square_quantile(annotated_peptides_quantiles_peptides[scan_index]))); } } + + for (auto & ph : pi.getHits()) + { + ph.setMetaValue("NuXL:QQ_TIC", QQ_TIC[scan_index].quantileOfValue(ph.getMetaValue("NuXL:total_MIC"))); + ph.setMetaValue("NuXL:QQ_EXPLAINED_FRACTION", QQ_EXPLAINED_FRACTION[scan_index].quantileOfValue(ph.getMetaValue("NuXL:explained_peak_fraction"))); + } + + + + } #endif From 90e5f4a6160835525cda00109fb5ae0ab5010d4a Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 17 Sep 2020 10:11:33 +0200 Subject: [PATCH 127/471] some cleanup - enabled nested cross-validation --- .../FILTERING/DATAREDUCTION/Deisotoper.cpp | 3 +- src/utils/OpenNuXL.cpp | 336 ++++-------------- 2 files changed, 70 insertions(+), 269 deletions(-) diff --git a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp index d71dd90eb37..2661c44a0bb 100644 --- a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp +++ b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp @@ -163,8 +163,7 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, has_min_isopeaks = (i >= min_isopeaks); break; } - -/* +/* // ratio of first isotopic peak to monoisotopic peak may not be too large if (i == 1 && old_spectrum[p].getIntensity() / old_spectrum[extensions.back()].getIntensity() > 10.0) { diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 790e5595f22..1e8ca2e834d 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -129,7 +129,7 @@ using namespace boost::accumulators; //#define FILTER_NO_ARBITRARY_TAG_PRESENT #define CALCULATE_LONGEST_TAG //#define MODDS_ON_ABY_IONS_ONLY -//#define SVM_RECALIBRATE +#define SVM_RECALIBRATE 1 //#define FILTER_RANKS 1 //#define CALCULATE_NUCLEOTIDE_TAGS 1 #define DONT_ACCUMULATE_PARTIAL_ION_SCORES 1 @@ -462,6 +462,8 @@ class OpenNuXL : static constexpr Size IA_RANK_INDEX = 1; static constexpr Size IA_DENOVO_TAG_INDEX = 2; protected: + /// percolator feature set + StringList feature_set_; void registerOptionsAndFlags_() override { @@ -2293,7 +2295,7 @@ static void scoreXLIons_( // deisotope Deisotoper::deisotopeAndSingleCharge(spec, - 0.03, + 0.01, false, 1, 3, false, @@ -2417,9 +2419,8 @@ static void scoreXLIons_( dist_file << mz << "\t" << peak_density.getBinIntensity(mz) << "\n"; } dist_file.close(); - - MzMLFile().store("debug_filtering.mzML", exp); #endif + if (debug_level_ > 10) MzMLFile().store("debug_filtering.mzML", exp); } void filterTopNAnnotations_(vector>& ahs, const Size top_hits) @@ -3638,57 +3639,6 @@ static void scoreXLIons_( search_parameters.fragment_mass_tolerance_ppm = getStringOption_("fragment:mass_tolerance_unit") == "ppm" ? true : false; search_parameters.digestion_enzyme = *ProteaseDB::getInstance()->getEnzyme(getStringOption_("peptide:enzyme")); - /* default features added in PercolatorAdapter: - * SpecId, ScanNr, ExpMass, CalcMass, mass, - * peplen, charge#min..#max, enzN, enzC, enzInt, dm, absdm - */ - StringList feature_set; - feature_set - << "NuXL:mass_error_p" - << "NuXL:err" - << "NuXL:total_loss_score" - << "NuXL:modds" - << "NuXL:immonium_score" - << "NuXL:precursor_score" - << "NuXL:MIC" - << "NuXL:Morph" - << "NuXL:total_MIC" - << "NuXL:ladder_score" - << "NuXL:sequence_score" - << "NuXL:total_Morph" - << "NuXL:total_HS" - << "NuXL:tag_XLed" - << "NuXL:tag_unshifted" - << "NuXL:tag_shifted" - << "NuXL:aminoacid_max_tag" - << "NuXL:aminoacid_id_to_max_tag_ratio" - << "nr_candidates" - << "NuXL:explained_peak_fraction" - << "NuXL:QQ_TIC" - << "NuXL:QQ_EXPLAINED_FRACTION" - << "NuXL:wTop50"; - - feature_set - << "NuXL:marker_ions_score" - << "NuXL:partial_loss_score" - << "NuXL:pl_MIC" - << "NuXL:pl_err" - << "NuXL:pl_Morph" - << "NuXL:pl_modds" - << "NuXL:pl_pc_MIC" - << "NuXL:pl_im_MIC"; - - feature_set - << "NuXL:isPhospho" - << "NuXL:isXL" - << "NuXL:score" - << "isotope_error" - << "variable_modifications" - << "precursor_intensity_log10" - << "NuXL:NA_MASS_z0" - << "NuXL:NA_length" - << "nucleotide_mass_tags"; - #ifdef OPENNUXL_SEPARATE_FEATURES for (auto & pi : peptide_ids) { @@ -3697,7 +3647,7 @@ static void scoreXLIons_( if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) { // fill XL related feature columns with zeros - for (const auto & s : feature_set) + for (const auto & s : feature_set_) { if (s.hasPrefix("NuXL")) ph.setMetaValue("XL_" + s, 0.0); } @@ -3720,27 +3670,11 @@ static void scoreXLIons_( // we duplicated the feature set auto XL_columns = feature_set; for (const auto& s : feature_set) { if (s.hasPrefix("NuXL")) XL_columns.push_back("XL_" + s); } - feature_set = XL_columns; + feature_set_ = XL_columns; #endif -#ifdef DANGEROUS_FEAUTURES - feature_set - << "CountSequenceIsTop" - << "CountSequenceCharges" - << "CountSequenceIsXL" - << "CountSequenceIsPeptide"; -#endif - - if (!purities.empty()) feature_set << "precursor_purity"; - - // one-hot encoding of cross-linked nucleotide - const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); - for (const auto& c : can_cross_link) - { - feature_set << String("NuXL:XL_" + String(c)); - } search_parameters.setMetaValue("feature_extractor", "TOPP_PSMFeatureExtractor"); - search_parameters.setMetaValue("extra_features", ListUtils::concatenate(feature_set, ",")); + search_parameters.setMetaValue("extra_features", ListUtils::concatenate(feature_set_, ",")); protein_ids[0].setSearchParameters(search_parameters); } @@ -4356,6 +4290,7 @@ static void scoreXLIons_( bool spectrumclusterfilter = find(filter.begin(), filter.end(), "spectrumclusterfilter") != filter.end(); bool pcrecalibration = find(filter.begin(), filter.end(), "pcrecalibration") != filter.end(); + if (pcrecalibration) { MSExperiment e; @@ -4426,8 +4361,8 @@ static void scoreXLIons_( << "-train-best-positive" << "-score_type" << "q-value" << "-post-processing-tdc" - << "-weights" << weights_out.toQString(); -// << "-nested-xval-bins" << "3"; + << "-weights" << weights_out.toQString() + << "-nested-xval-bins" << "3"; //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); @@ -4666,7 +4601,7 @@ static void scoreXLIons_( // read list of nucleotides that can directly cross-link // these are responsible for shifted fragment ions. Their fragment adducts thus determine which shifts will be observed on b-,a-,y-ions - String can_cross_link = getStringOption_("RNPxl:can_cross_link"); + const String& can_cross_link = getStringOption_("RNPxl:can_cross_link"); for (const auto& c : can_cross_link) { can_xl_.insert(c); } StringList modifications = getStringList_("RNPxl:modifications"); @@ -4735,6 +4670,61 @@ static void scoreXLIons_( } } // free spectra + ///////////////////////////////////////////////////////////////////////// + // define percolator feature set + /* default features added in PercolatorAdapter: + * SpecId, ScanNr, ExpMass, CalcMass, mass, + * peplen, charge#min..#max, enzN, enzC, enzInt, dm, absdm + */ + feature_set_ + << "NuXL:mass_error_p" + << "NuXL:err" + << "NuXL:total_loss_score" + << "NuXL:modds" + << "NuXL:immonium_score" + << "NuXL:precursor_score" + << "NuXL:MIC" + << "NuXL:Morph" + << "NuXL:total_MIC" + << "NuXL:ladder_score" + << "NuXL:sequence_score" + << "NuXL:total_Morph" + << "NuXL:total_HS" + << "NuXL:tag_XLed" + << "NuXL:tag_unshifted" + << "NuXL:tag_shifted" + << "NuXL:aminoacid_max_tag" + << "NuXL:aminoacid_id_to_max_tag_ratio" + << "nr_candidates" + << "NuXL:explained_peak_fraction" + << "NuXL:QQ_TIC" + << "NuXL:QQ_EXPLAINED_FRACTION" + << "NuXL:wTop50" + + << "NuXL:marker_ions_score" + << "NuXL:partial_loss_score" + << "NuXL:pl_MIC" + << "NuXL:pl_err" + << "NuXL:pl_Morph" + << "NuXL:pl_modds" + << "NuXL:pl_pc_MIC" + << "NuXL:pl_im_MIC" + + << "NuXL:isPhospho" + << "NuXL:isXL" + << "NuXL:score" + << "isotope_error" + << "variable_modifications" + << "precursor_intensity_log10" + << "NuXL:NA_MASS_z0" + << "NuXL:NA_length" + << "nucleotide_mass_tags"; + + if (!purities.empty()) feature_set_ << "precursor_purity"; + + // one-hot encoding of cross-linked nucleotide + for (const auto& c : can_cross_link) { feature_set_ << String("NuXL:XL_" + String(c)); } + PeakFileOptions options; options.clearMSLevels(); options.addMSLevel(2); @@ -5758,6 +5748,7 @@ static void scoreXLIons_( map XL_t; map XL_d; + // map scores to index (sorted) for (size_t index = 0; index != peptide_ids.size(); ++index) { if (peptide_ids[index].getHits().empty()) continue; @@ -5812,195 +5803,6 @@ static void scoreXLIons_( SimpleSVM::PredictorMap predictors; map labels; -/* - StringList feature_set; - feature_set - << "NuXL:mass_error_p" - << "NuXL:err" - << "NuXL:total_loss_score" - << "NuXL:modds" - << "NuXL:immonium_score" - << "NuXL:precursor_score" - << "NuXL:MIC" - << "NuXL:Morph" - << "NuXL:total_MIC" - << "NuXL:ladder_score" - << "NuXL:sequence_score" - << "NuXL:total_Morph" - << "NuXL:total_HS" - << "NuXL:tag_XLed" - << "NuXL:tag_unshifted" - << "NuXL:tag_shifted" - << "NuXL:aminoacid_max_tag" - << "NuXL:aminoacid_id_to_max_tag_ratio" - << "nr_candidates" - << "NuXL:rank_product" - << "NuXL:wTop50" - << "NuXL:marker_ions_score" - << "NuXL:partial_loss_score" - << "NuXL:pl_MIC" - << "NuXL:pl_err" - << "NuXL:pl_Morph" - << "NuXL:pl_modds" - << "NuXL:pl_pc_MIC" - << "NuXL:pl_im_MIC" - << "NuXL:isPhospho" - << "NuXL:isXL" - << "NuXL:score" - << "isotope_error" - << "variable_modifications" - << "precursor_intensity_log10" - << "NuXL:NA_MASS_z0" - << "NuXL:NA_length" - << "nucleotide_mass_tags"; -*/ - - // feature set that can be calculated on-line during scoring - StringList feature_set; - feature_set - << "NuXL:mass_error_p" - << "isotope_error" - << "NuXL:err" - << "NuXL:total_loss_score" - << "NuXL:immonium_score" - << "NuXL:precursor_score" - << "NuXL:MIC" - << "NuXL:Morph" - << "NuXL:modds" - << "NuXL:partial_loss_score" - << "NuXL:pl_MIC" - << "NuXL:pl_err" - << "NuXL:pl_Morph" - << "NuXL:pl_im_MIC" - << "NuXL:pl_modds" - << "NuXL:pl_pc_MIC" - << "NuXL:total_MIC" - << "NuXL:marker_ions_score" - << "NuXL:ladder_score" - << "NuXL:sequence_score" - << "NuXL:tag_XLed" - << "NuXL:tag_unshifted" - << "NuXL:tag_shifted" - << "NuXL:explained_peak_fraction" - << "NuXL:isXL" - << "NuXL:wTop50"; - - -/* - * -Feature weights: -NuXL:NA_MASS_z0 1.30088 -NuXL:NA_length -1.40758 -NuXL:aminoacid_id_to_max_tag_ratio 0.92732 -NuXL:aminoacid_max_tag -0.744218 -(NuXL:score 3.74526) -(score 3.74526) -NuXL:total_HS 3.90137 -NuXL:total_Morph 2.24353 - -NuXL:err 0.118611 -NuXL:immonium_score 1.70748 -NuXL:modds 1.76435 -NuXL:isXL -2.21505 -NuXL:ladder_score 2.02304 -NuXL:marker_ions_score 1.26403 -NuXL:mass_error_p 0.253748 -NuXL:partial_loss_score 0.587148 -NuXL:pl_modds 0.324605 -NuXL:pl_pc_MIC 0.176533 -NuXL:pl_im_MIC -0.2534 -NuXL:pl_MIC -0.177937 -NuXL:pl_Morph -1.58991 -NuXL:pl_err -0.0100689 -NuXL:total_loss_score 3.73413 -NuXL:MIC 0.564764 -NuXL:Morph 3.04116 -NuXL:sequence_score -1.59204 -NuXL:tag_XLed 1.63176 -NuXL:tag_shifted -0.176563 -NuXL:tag_unshifted 3.73061 -NuXL:total_MIC 0.575831 -NuXL:wTop50 -0.137687 -length 0.195985 -NuXL:precursor_score -0.513751 -NuXL:rank_product 0.349211 - - -nr_candidates 0.453777 -nucleotide_mass_tags 0.00899349 -precursor_intensity_log10 -0.383641 -variable_modifications -0.0944707 - - * */ - -/* - * mean ppm error: 0.0569701 sd: 0.447449 5*sd: 2.23725 - * Peptide (target/decoy) XL (target/decoy): - * 3975 3011 9613 4045 - * Predictor 'isotope_error' is uninformative. - * Training SVM on 12044 observations. Classes: - * - '0': 6022 observations - * - '1': 6022 observations - * Running cross-validation to find optimal SVM parameters... - * Best cross-validation performance: 83.4772% correct - * Best SVM parameters: log2_C = 5, log2_gamma = 0 - * Number of support vectors in the final model: 4252 - * Feature weights: - * NuXL:MIC 0.00317232 - * NuXL:Morph -5.67908 - * NuXL:err 0.0074405 - * NuXL:immonium_score 3.87159 - * NuXL:isXL -2.8901 - * NuXL:ladder_score 2.09632 - * NuXL:marker_ions_score 2.53656 - * NuXL:mass_error_p 0.189849 - * NuXL:modds 9.42353 - * NuXL:partial_loss_score 4.22367 - * NuXL:pl_MIC 0.0770935 - * NuXL:pl_Morph -4.25703 - * NuXL:pl_err -0.059863 - * NuXL:pl_im_MIC -0.367491 - * NuXL:pl_modds 2.29632 - * NuXL:pl_pc_MIC 1.13888 - * NuXL:precursor_score -0.597915 - * NuXL:rank_product 0.460718 - * NuXL:sequence_score -4.68762 - * NuXL:tag_XLed 2.61103 - * NuXL:tag_shifted -0.10144 - * NuXL:tag_unshifted 10.8324 - * NuXL:total_MIC 0.836277 - * NuXL:total_loss_score 34.8899 - * NuXL:wTop50 -0.248061 - * length 0.00656285 - * Feature scaling: - * NuXL:MIC 0.00693372 0.798143 - * NuXL:Morph 2.00693 50.6892 - * NuXL:err 1.8356e-05 0.0286427 - * NuXL:immonium_score 0 0.0684432 - * NuXL:isXL 0 1 - * NuXL:ladder_score 0.0381864 1.11803 - * NuXL:marker_ions_score 0 0.12167 - * NuXL:mass_error_p 0.6439 1 - * NuXL:modds 3.37613e-07 22.9923 - * NuXL:partial_loss_score 0 38.5117 - * NuXL:pl_MIC 0 0.352322 - * NuXL:pl_Morph 0 20.2243 - * NuXL:pl_err 0.000214374 0.02 - * NuXL:pl_im_MIC 0 0.115692 - * NuXL:pl_modds 0 7.26252 - * NuXL:pl_pc_MIC 0 0.33534 - * NuXL:precursor_score 0 0.299693 - * NuXL:rank_product 1 149.905 - * NuXL:sequence_score 0.0218818 1.11803 - * NuXL:tag_XLed 0 21 - * NuXL:tag_shifted 0 17 - * NuXL:tag_unshifted 1 33 - * NuXL:total_MIC 0.0100453 0.844876 - * NuXL:total_loss_score 0.106861 119.842 - * NuXL:wTop50 2 229 - * length 6 48 - */ - // copy all scores in predictors ("score" + all from feature_set). // Only add labels for balanced training set size_t current_row(0); @@ -6014,7 +5816,7 @@ variable_modifications -0.0944707 double score = ph.getScore(); // predictors["score"].push_back(score); predictors["length"].push_back(ph.getSequence().size()); - for (auto & f : feature_set) + for (auto & f : feature_set_) { double value = ph.getMetaValue(f); predictors[f].push_back(value); From 006f3f0c0bb47c4494b0aa22b4dbc0f30203661e Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 22 Sep 2020 16:41:36 +0200 Subject: [PATCH 128/471] updates SSE to include other scores for percolator --- .../ANALYSIS/ID/SimpleSearchEngineAlgorithm.h | 3 + .../OpenMS/ANALYSIS/RNPXL/HyperScore.h | 18 +++++ src/openms/include/OpenMS/CONCEPT/Constants.h | 11 +++ .../ID/SimpleSearchEngineAlgorithm.cpp | 34 +++++++-- .../source/ANALYSIS/RNPXL/HyperScore.cpp | 76 +++++++++++++++++++ src/openms/source/CHEMISTRY/ResidueDB.cpp | 1 + src/openms/source/CONCEPT/Constants.cpp | 6 ++ src/utils/OpenNuXL.cpp | 8 +- 8 files changed, 151 insertions(+), 6 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h b/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h index 641396ad69c..9cd02533348 100644 --- a/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h +++ b/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h @@ -74,6 +74,9 @@ class OPENMS_DLLAPI SimpleSearchEngineAlgorithm : StringView sequence; SignedSize peptide_mod_index; ///< enumeration index of the non-RNA peptide modification double score = 0; ///< main score + double prefix_fraction = 0; ///< fraction of annotated b-ions + double suffix_fraction = 0; ///< fraction of annotated y-ions + double mean_error = 0.0; ///< mean absolute fragment mass error std::vector fragment_annotations; static bool hasBetterScore(const AnnotatedHit_& a, const AnnotatedHit_& b) { diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h index 5d177f62fd4..60c1023e7e7 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/HyperScore.h @@ -66,6 +66,24 @@ struct OPENMS_DLLAPI HyperScore bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum); + + /** @brief compute the (ln transformed) X!Tandem HyperScore + * overload that returns some additional information on the match + */ + struct PSMDetail + { + size_t matched_b_ions = 0; + size_t matched_y_ions = 0; + double mean_error = 0.0; + }; + + static double computeWithDetail(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const PeakSpectrum& theo_spectrum, + PSMDetail& d + ); + /* @brief compute the (ln transformed) X!Tandem HyperScore only matching peaks that match in charge * 1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated * 2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions diff --git a/src/openms/include/OpenMS/CONCEPT/Constants.h b/src/openms/include/OpenMS/CONCEPT/Constants.h index 6ca53fbc108..7fcc5d7b60c 100644 --- a/src/openms/include/OpenMS/CONCEPT/Constants.h +++ b/src/openms/include/OpenMS/CONCEPT/Constants.h @@ -279,6 +279,17 @@ namespace OpenMS */ extern OPENMS_DLLAPI const std::string FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM; + /** User parameter name for the fraction of matched prefix ions in a PSM + String + */ + extern OPENMS_DLLAPI const std::string MATCHED_PREFIX_IONS_FRACTION; + + /** User parameter name for the fraction of matched suffix ions in a PSM + String + */ + extern OPENMS_DLLAPI const std::string MATCHED_SUFFIX_IONS_FRACTION; + + /** User parameter name for fragment annotations String */ diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index 648f1a005d6..cfdb4bbf976 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -134,7 +134,13 @@ namespace OpenMS defaults_.setValidStrings("decoys", {"true","false"} ); defaults_.setValue("annotate:PSM", StringList{}, "Annotations added to each PSM."); - defaults_.setValidStrings("annotate:PSM", StringList{Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM, Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM}); + defaults_.setValidStrings("annotate:PSM", + StringList{ + Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM, + Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM, + Constants::UserParam::MATCHED_PREFIX_IONS_FRACTION, + Constants::UserParam::MATCHED_SUFFIX_IONS_FRACTION} + ); defaults_.setSectionDescription("annotate", "Annotation Options"); defaults_.setValue("peptide:min_size", 7, "Minimum size a peptide must have after digestion to be considered in the search."); @@ -272,10 +278,11 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, annotated_hits.shrink_to_fit(); } - bool annotation_precursor_error_ppm = std::find(annotate_psm_.begin(), annotate_psm_.end(), Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM) != annotate_psm_.end(); bool annotation_fragment_error_ppm = std::find(annotate_psm_.begin(), annotate_psm_.end(), Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM) != annotate_psm_.end(); - + bool annotation_prefix_fraction = std::find(annotate_psm_.begin(), annotate_psm_.end(), Constants::UserParam::MATCHED_PREFIX_IONS_FRACTION) != annotate_psm_.end(); + bool annotation_suffix_fraction = std::find(annotate_psm_.begin(), annotate_psm_.end(), Constants::UserParam::MATCHED_SUFFIX_IONS_FRACTION) != annotate_psm_.end(); +// double annotation_mean_error = #pragma omp parallel for for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) { @@ -339,6 +346,17 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, double ppm_difference = Math::getPPM(mz, theo_mz); ph.setMetaValue(Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM, ppm_difference); } + + if (annotation_prefix_fraction) + { + ph.setMetaValue(Constants::UserParam::MATCHED_PREFIX_IONS_FRACTION, ah.prefix_fraction); + } + + if (annotation_suffix_fraction) + { + ph.setMetaValue(Constants::UserParam::MATCHED_SUFFIX_IONS_FRACTION, ah.suffix_fraction); + } + // store PSM phs.push_back(ph); } @@ -385,10 +403,12 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, search_parameters.fragment_mass_tolerance_ppm = fragment_mass_tolerance_unit_ppm == "ppm"; search_parameters.digestion_enzyme = *ProteaseDB::getInstance()->getEnzyme(enzyme); - // for post-processing + // add additional percolator features or post-processing search_parameters.setMetaValue("feature_extractor", "TOPP_PSMFeatureExtractor"); StringList feature_set{"score"}; if (annotation_fragment_error_ppm) feature_set.push_back(Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM); + if (annotation_prefix_fraction) feature_set.push_back(Constants::UserParam::MATCHED_PREFIX_IONS_FRACTION); + if (annotation_suffix_fraction) feature_set.push_back(Constants::UserParam::MATCHED_SUFFIX_IONS_FRACTION); search_parameters.setMetaValue("extra_features", ListUtils::concatenate(feature_set, ",")); protein_ids[0].setSearchParameters(search_parameters); @@ -599,7 +619,8 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, const Size& scan_index = low_it->second; const PeakSpectrum& exp_spectrum = spectra[scan_index]; // const int& charge = exp_spectrum.getPrecursors()[0].getCharge(); - const double& score = HyperScore::compute(fragment_mass_tolerance_, fragment_mass_tolerance_unit_ppm, exp_spectrum, theo_spectrum); + HyperScore::PSMDetail detail; + const double& score = HyperScore::computeWithDetail(fragment_mass_tolerance_, fragment_mass_tolerance_unit_ppm, exp_spectrum, theo_spectrum, detail); if (score == 0) { continue; } // no hit? @@ -608,6 +629,9 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, ah.sequence = c; ah.peptide_mod_index = mod_pep_idx; ah.score = score; + ah.prefix_fraction = (double)detail.matched_b_ions/(double)c.size(); + ah.suffix_fraction = (double)detail.matched_y_ions/(double)c.size(); + ah.mean_error = detail.mean_error; #ifdef _OPENMP omp_set_lock(&(annotated_hits_lock[scan_index])); diff --git a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp index 22ca291bdd5..15f271c43a3 100644 --- a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp @@ -125,6 +125,82 @@ namespace OpenMS return hyperScore; } + double HyperScore::computeWithDetail(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum, PSMDetail& d) + { + if (exp_spectrum.size() < 1 || theo_spectrum.size() < 1) + { + std::cout << "Warning: HyperScore: One of the given spectra is empty." << std::endl; + return 0.0; + } + + // TODO this assumes only one StringDataArray is present and it is the right one + const PeakSpectrum::StringDataArray* ion_names; + if (theo_spectrum.getStringDataArrays().size() > 0) + { + ion_names = &theo_spectrum.getStringDataArrays()[0]; + } + else + { + std::cout << "Error: HyperScore: Theoretical spectrum without StringDataArray (\"IonNames\" annotation) provided." << std::endl; + return 0.0; + } + + int y_ion_count = 0; + int b_ion_count = 0; + double dot_product = 0.0; + double abs_error = 0.0; + if (fragment_mass_tolerance_unit_ppm) + { + MatchedIterator it(theo_spectrum, exp_spectrum, fragment_mass_tolerance); + for (; it != it.end(); ++it) + { + abs_error += Math::getPPMAbs((*it).getMZ(), it.ref().getMZ()); + dot_product += (*it).getIntensity() * it.ref().getIntensity(); /* * mass_error */; + // fragment annotations in XL-MS data are more complex and do not start with the ion type, but the ion type always follows after a $ + auto i = it.refIdx(); + if ((*ion_names)[i][0] == 'y' || (*ion_names)[i].hasSubstring("$y")) + { + ++y_ion_count; + } + else if ((*ion_names)[i][0] == 'b' || (*ion_names)[i].hasSubstring("$b")) + { + ++b_ion_count; + } + } + } + else + { + MatchedIterator it(theo_spectrum, exp_spectrum, fragment_mass_tolerance); + for (; it != it.end(); ++it) + { + abs_error += abs((*it).getMZ() - it.ref().getMZ()); + dot_product += (*it).getIntensity() * it.ref().getIntensity(); /* * mass_error */; + // fragment annotations in XL-MS data are more complex and do not start with the ion type, but the ion type always follows after a $ + auto i = it.refIdx(); + if ((*ion_names)[i][0] == 'y' || (*ion_names)[i].hasSubstring("$y")) + { + ++y_ion_count; + } + else if ((*ion_names)[i][0] == 'b' || (*ion_names)[i].hasSubstring("$b")) + { + ++b_ion_count; + } + } + } + // inefficient: calculates logs repeatedly + //const double yFact = logfactorial_(y_ion_count); + //const double bFact = logfactorial_(b_ion_count); + //const double hyperScore = log1p(dot_product) + yFact + bFact; + + const int i_min = std::min(y_ion_count, b_ion_count); + const int i_max = std::max(y_ion_count, b_ion_count); + const double hyperScore = log1p(dot_product) + 2*logfactorial_(i_min) + logfactorial_(i_max, i_min + 1); + d.matched_b_ions = b_ion_count; + d.matched_y_ions = y_ion_count; + d.mean_error = (b_ion_count + y_ion_count) > 0 ? abs_error / (double)(b_ion_count + y_ion_count) : 0.0; + return hyperScore; + } + double HyperScore::compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, diff --git a/src/openms/source/CHEMISTRY/ResidueDB.cpp b/src/openms/source/CHEMISTRY/ResidueDB.cpp index 399a8ed9d07..a2664250f23 100644 --- a/src/openms/source/CHEMISTRY/ResidueDB.cpp +++ b/src/openms/source/CHEMISTRY/ResidueDB.cpp @@ -53,6 +53,7 @@ namespace OpenMS { ResidueDB::ResidueDB() { + cout << "Loading residue database from file." << endl; readResiduesFromFile_("CHEMISTRY/Residues.xml"); buildResidueNames_(); } diff --git a/src/openms/source/CONCEPT/Constants.cpp b/src/openms/source/CONCEPT/Constants.cpp index e8f7daa4ca0..07dbf191753 100644 --- a/src/openms/source/CONCEPT/Constants.cpp +++ b/src/openms/source/CONCEPT/Constants.cpp @@ -172,6 +172,12 @@ namespace OpenMS // User parameter name for precursor mz error in ppm const std::string FRAGMENT_ANNOTATION_USERPARAM = "fragment_annotation"; + // User parameter name for the fraction of prefix ions that have been matched + const std::string MATCHED_PREFIX_IONS_FRACTION = "matched_prefix_ions_fraction"; + + // User parameter name for the fraction of suffix ions that have been matched + const std::string MATCHED_SUFFIX_IONS_FRACTION = "matched_suffix_ions_fraction"; + // User parameter name for the spectrum reference in PeptideIdentification (is is not yet treated as a class attribute) const std::string SPECTRUM_REFERENCE = "spectrum_reference"; diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 1e8ca2e834d..a8dc34e542c 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -4331,7 +4331,13 @@ static void scoreXLIons_( p.setValue("precursor:isotopes", IntList{0, 1}); p.setValue("decoys", generate_decoys ? "true" : "false"); p.setValue("enzyme", getStringOption_("peptide:enzyme")); - p.setValue("annotate:PSM", StringList{Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM, Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM}); + p.setValue("annotate:PSM", + StringList{ + Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM, + Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM, + Constants::UserParam::MATCHED_PREFIX_IONS_FRACTION, + Constants::UserParam::MATCHED_SUFFIX_IONS_FRACTION + }); sse.setParameters(p); cout << "Running autotune..." << endl; sse.search(in_mzml, in_db, prot_ids, pep_ids); From 3f092541093ecbfb92f44f39cb10d77a82d1ce50 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 11 Nov 2020 14:33:38 +0100 Subject: [PATCH 129/471] fix some NuXL deisotoper errors --- .../FILTERING/DATAREDUCTION/Deisotoper.cpp | 50 ++- .../openms/data/Deisotoper_input1.mzML | 255 ++++++++++++++ .../openms/data/Deisotoper_input2.mzML | 314 +++++++++++++++++ .../openms/data/Deisotoper_output1.mzML | 261 ++++++++++++++ .../openms/data/Deisotoper_output2.mzML | 320 ++++++++++++++++++ .../openms/source/Deisotoper_test.cpp | 39 +++ src/utils/OpenNuXL.cpp | 2 +- 7 files changed, 1235 insertions(+), 6 deletions(-) create mode 100644 src/tests/class_tests/openms/data/Deisotoper_input1.mzML create mode 100644 src/tests/class_tests/openms/data/Deisotoper_input2.mzML create mode 100644 src/tests/class_tests/openms/data/Deisotoper_output1.mzML create mode 100644 src/tests/class_tests/openms/data/Deisotoper_output2.mzML diff --git a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp index 2661c44a0bb..56480988e53 100644 --- a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp +++ b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp @@ -36,6 +36,7 @@ #include #include #include +#include #include #include @@ -67,6 +68,9 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, OPENMS_PRETTY_FUNCTION, "Minimum/maximum number of isotopic peaks must be at least 2 (and min_isopeaks <= max_isopeaks)."); } + + const bool preserve_high_intensity_peaks = true; + Size charge_index(0); Size iso_peak_count_index(0); @@ -100,6 +104,29 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, std::vector iso_peak_count(old_spectrum.size(), 1); int feature_number = 0; + MSSpectrum high_intensity_peaks; + if (preserve_high_intensity_peaks) // TODO: document what happens with keep_only_deisotoped=true as it might add high-intensity peaks without charge (=> might lead to surprises if that option is taken) + { + high_intensity_peaks = spec; + // find high intensity peaks + WindowMower window_mower_filter; + Param filter_param = window_mower_filter.getParameters(); + filter_param.setValue("windowsize", 4.0, "The size of the sliding window along the m/z axis."); + filter_param.setValue("peakcount", 1, "The number of peaks that should be kept."); + filter_param.setValue("movetype", "jump", "Whether sliding window (one peak steps) or jumping window (window size steps) should be used."); + window_mower_filter.setParameters(filter_param); + + // add peak indices so we know what is retained after filtering + high_intensity_peaks.getIntegerDataArrays().resize(high_intensity_peaks.getIntegerDataArrays().size() + 1); + high_intensity_peaks.getIntegerDataArrays().back().setName("index"); + for (size_t index = 0; index != high_intensity_peaks.size(); ++index) + { + high_intensity_peaks.getIntegerDataArrays().back().push_back(index); + } + // filter peaks and integer data arrays + window_mower_filter.filterPeakSpectrum(high_intensity_peaks); + } + std::vector extensions; bool has_precursor_data(false); @@ -141,7 +168,7 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, } extensions.clear(); - extensions.push_back(current_peak); + extensions.push_back(current_peak); // add current peak as start of extensions for (unsigned int i = 1; i < max_isopeaks; ++i) { const double expected_mz = current_mz + static_cast(i) * Constants::C13C12_MASSDIFF_U / static_cast(q); @@ -163,14 +190,14 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, has_min_isopeaks = (i >= min_isopeaks); break; } -/* - // ratio of first isotopic peak to monoisotopic peak may not be too large + + // ratio of first isotopic peak to monoisotopic peak may not be too large otherwise it might be just a satelite peak (e.g, amidation) if (i == 1 && old_spectrum[p].getIntensity() / old_spectrum[extensions.back()].getIntensity() > 10.0) { has_min_isopeaks = (i >= min_isopeaks); break; - } -*/ + } + // averagine check passed or skipped extensions.push_back(p); if (annotate_iso_peak_count) @@ -235,8 +262,21 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, spec[i].setMZ(spec[i].getMZ() * z - (z - 1) * Constants::PROTON_MASS_U); } select_idx.push_back(i); + } + if (preserve_high_intensity_peaks) + { + // add peak index if we want to keep that peak + for (size_t i = 0; i != high_intensity_peaks.size(); ++i) + { + int peak_index = high_intensity_peaks.getIntegerDataArrays().back()[i]; + if (std::find(select_idx.begin(), select_idx.end(), peak_index) == select_idx.end()) + { + select_idx.push_back(peak_index); + } + } } + // properly subsets all datapoints (incl. dataArrays) spec.select(select_idx); spec.sortByPosition(); diff --git a/src/tests/class_tests/openms/data/Deisotoper_input1.mzML b/src/tests/class_tests/openms/data/Deisotoper_input1.mzML new file mode 100644 index 00000000000..9bcc48667e7 --- /dev/null +++ b/src/tests/class_tests/openms/data/Deisotoper_input1.mzML @@ -0,0 +1,255 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + Cyk/qfZmhEALKT+p9maEQA== + + + + + + rAPZSqwD2Uo= + + + + + + + + + 12050 + 24173 + + + 34089 + + +35533 +0 + \ No newline at end of file diff --git a/src/tests/class_tests/openms/source/Deisotoper_test.cpp b/src/tests/class_tests/openms/source/Deisotoper_test.cpp index e41c8ec7786..f1c71295671 100644 --- a/src/tests/class_tests/openms/source/Deisotoper_test.cpp +++ b/src/tests/class_tests/openms/source/Deisotoper_test.cpp @@ -43,6 +43,7 @@ #include #include #include +#include /////////////////////////// @@ -152,6 +153,44 @@ START_SECTION(static void deisotopeAndSingleChargeMSSpectrum(MSSpectrum& in, MSSpectrum theo1_noiso; spec_generator.getSpectrum(theo1_noiso, peptide1, 1, 2); // charge 1..2 TEST_EQUAL(theo1.size(), theo1_noiso.size()); // same number of peaks after deisotoping + + // load data with small intensity satellite peaks (e.g., amidation) + MSExperiment input1; + MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("Deisotoper_input1.mzML"), input1); + Deisotoper::deisotopeAndSingleCharge(input1[0], + 0.01, // Da + false, + 1, + 3, + false, + 2, + 10, + false, + true, + false, // no iso peak count annotation + true, // decreasing isotope model + 2, // enforce only starting from second peak + true); + MzMLFile().store(OPENMS_GET_TEST_DATA_PATH("Deisotoper_output1.mzML"), input1); + + // load data with small intensity satellite peaks (e.g., amidation) + MSExperiment input2; + MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("Deisotoper_input2.mzML"), input2); + Deisotoper::deisotopeAndSingleCharge(input2[0], + 0.01, // Da + false, + 1, + 3, + false, + 2, + 10, + false, + true, + false, // no iso peak count annotation + true, // decreasing isotope model + 2, // enforce only starting from second peak + true); + MzMLFile().store(OPENMS_GET_TEST_DATA_PATH("Deisotoper_output2.mzML"), input2); } END_SECTION diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index a8dc34e542c..95599fe0beb 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -129,7 +129,7 @@ using namespace boost::accumulators; //#define FILTER_NO_ARBITRARY_TAG_PRESENT #define CALCULATE_LONGEST_TAG //#define MODDS_ON_ABY_IONS_ONLY -#define SVM_RECALIBRATE 1 +//#define SVM_RECALIBRATE 1 //#define FILTER_RANKS 1 //#define CALCULATE_NUCLEOTIDE_TAGS 1 #define DONT_ACCUMULATE_PARTIAL_ION_SCORES 1 From 0f19511549efd6c03fdcaf534f7ca1bd57661f2f Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Sat, 21 Nov 2020 11:02:44 +0100 Subject: [PATCH 130/471] [FIX] Deisotoper now also keeps monoisotopic if deamidated peaks are present --- .../FILTERING/DATAREDUCTION/Deisotoper.cpp | 113 ++++++++++++++++-- .../openms/data/Deisotoper_output1.mzML | 18 +-- .../openms/data/Deisotoper_output2.mzML | 20 ++-- src/utils/OpenNuXL.cpp | 30 ++++- 4 files changed, 151 insertions(+), 30 deletions(-) diff --git a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp index 56480988e53..3608c9fe822 100644 --- a/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp +++ b/src/openms/source/FILTERING/DATAREDUCTION/Deisotoper.cpp @@ -104,6 +104,17 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, std::vector iso_peak_count(old_spectrum.size(), 1); int feature_number = 0; + std::vector extensions; + + bool has_precursor_data(false); + double precursor_mass(0); + if (old_spectrum.getPrecursors().size() == 1) + { + has_precursor_data = true; + int precursor_charge = old_spectrum.getPrecursors()[0].getCharge(); + precursor_mass = (old_spectrum.getPrecursors()[0].getMZ() * precursor_charge) - (Constants::PROTON_MASS * precursor_charge); + } + MSSpectrum high_intensity_peaks; if (preserve_high_intensity_peaks) // TODO: document what happens with keep_only_deisotoped=true as it might add high-intensity peaks without charge (=> might lead to surprises if that option is taken) { @@ -125,19 +136,103 @@ void Deisotoper::deisotopeAndSingleCharge(MSSpectrum& spec, } // filter peaks and integer data arrays window_mower_filter.filterPeakSpectrum(high_intensity_peaks); - } - std::vector extensions; + // use high intensity peaks as seeds + for (size_t i = 0; i != high_intensity_peaks.size(); ++i) + { + size_t current_peak = high_intensity_peaks.getIntegerDataArrays().back()[i]; - bool has_precursor_data(false); - double precursor_mass(0); - if (old_spectrum.getPrecursors().size() == 1) - { - has_precursor_data = true; - int precursor_charge = old_spectrum.getPrecursors()[0].getCharge(); - precursor_mass = (old_spectrum.getPrecursors()[0].getMZ() * precursor_charge) - (Constants::PROTON_MASS * precursor_charge); + // deconvolve with high intensity peaks as seed + // TODO: remove duplication + const double current_mz = old_spectrum[current_peak].getMZ(); + if (add_up_intensity) + { + mono_iso_peak_intensity[current_peak] = old_spectrum[current_peak].getIntensity(); + } + + for (int q = max_charge; q >= min_charge; --q) // important: test charge hypothesis from high to low + { + // try to extend isotopes from mono-isotopic peak + // if extension larger then min_isopeaks possible: + // - save charge q in mono_isotopic_peak[] + // - annotate_charge all isotopic peaks with feature number + if (features[current_peak] == -1) // only process peaks which have no assigned feature number + { + bool has_min_isopeaks = true; + const double tolerance_dalton = fragment_unit_ppm ? Math::ppmToMass(fragment_tolerance, current_mz) : fragment_tolerance; + + // do not bother testing charges q (and masses m) with: m/q > precursor_mass/q (or m > precursor_mass) + if (has_precursor_data) + { + double current_theo_mass = (current_mz * q) - (Constants::PROTON_MASS * q); + if (current_theo_mass > (precursor_mass + tolerance_dalton)) + { + continue; + } + } + + extensions.clear(); + extensions.push_back(current_peak); // add current peak as start of extensions + for (unsigned int i = 1; i < max_isopeaks; ++i) + { + const double expected_mz = current_mz + static_cast(i) * Constants::C13C12_MASSDIFF_U / static_cast(q); + const int p = old_spectrum.findNearest(expected_mz, tolerance_dalton); + if (p == -1) // test for missing peak + { + has_min_isopeaks = (i >= min_isopeaks); + break; + } + else + { + // Possible improvement: include proper averagine model filtering + // for now start at the peak with i = start_intensity_check to test hypothesis + // if start_intensity_check = 0 or 1, start checking by comparing monoisotopic and second isotopic peak + // if start_intensity_check = 2, start checking by comparing second isotopic peak with the third, etc. + // Note: this is a common approach used in several other search engines + if (use_decreasing_model && (i >= start_intensity_check) && (old_spectrum[p].getIntensity() > old_spectrum[extensions.back()].getIntensity())) + { + has_min_isopeaks = (i >= min_isopeaks); + break; + } + + // ratio of first isotopic peak to monoisotopic peak may not be too large otherwise it might be just a satelite peak (e.g, amidation) + if (i == 1 && old_spectrum[p].getIntensity() / old_spectrum[extensions.back()].getIntensity() > 10.0) + { + has_min_isopeaks = (i >= min_isopeaks); + break; + } + + // averagine check passed or skipped + extensions.push_back(p); + if (annotate_iso_peak_count) + { + iso_peak_count[current_peak] = i + 1; // with "+ 1" the monoisotopic peak is counted as well + } + } + } + + if (has_min_isopeaks) + { + // std::cout << "min peaks at " << current_mz << " " << " extensions: " << extensions.size() << std::endl; + mono_isotopic_peak[current_peak] = q; + for (unsigned int i = 0; i != extensions.size(); ++i) + { + features[extensions[i]] = feature_number; + // monoisotopic peak intensity is already set above, add up the other intensities here + if (add_up_intensity && (i != 0)) + { + mono_iso_peak_intensity[current_peak] += old_spectrum[extensions[i]].getIntensity(); + } + } + ++feature_number; + } + } + } + } } + + // deisotope on all peaks for (size_t current_peak = 0; current_peak != old_spectrum.size(); ++current_peak) { const double current_mz = old_spectrum[current_peak].getMZ(); diff --git a/src/tests/class_tests/openms/data/Deisotoper_output1.mzML b/src/tests/class_tests/openms/data/Deisotoper_output1.mzML index d9b883ad700..01a56a41630 100644 --- a/src/tests/class_tests/openms/data/Deisotoper_output1.mzML +++ b/src/tests/class_tests/openms/data/Deisotoper_output1.mzML @@ -152,7 +152,7 @@ - + @@ -196,23 +196,23 @@ - + - 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@@ -309,12 +309,12 @@ 12050 - 24173 + 24121 - 34089 + 34037 -35533 +35481 0 \ No newline at end of file diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 95599fe0beb..f508d9434d8 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -2987,6 +2987,13 @@ static void scoreXLIons_( exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], ppm_error_array); + #ifdef OPENUXL_DEBUG + for (size_t i = 0; i != exp_spectrum.size(); ++i) + { + OPENMS_LOG_DEBUG << "exp: " << exp_spectrum[i].getMZ() << "\t" << exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX][i] << endl; + } + #endif + const PeakSpectrum::StringDataArray& partial_loss_annotations = partial_loss_spectrum.getStringDataArrays()[0]; const PeakSpectrum::IntegerDataArray& partial_loss_charges = partial_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX]; @@ -2996,6 +3003,13 @@ static void scoreXLIons_( continue; } + /* uncomment to write all annotations to a file(only makes sense if a single spectrum is searched) + MSExperiment tmp_exp; + tmp_exp.addSpectrum(total_loss_spectrum); + tmp_exp.addSpectrum(partial_loss_spectrum); + MzMLFile().store("theoretical_loss_spectrum.mzML", tmp_exp); + */ + for (auto pair_it = alignment.begin(); pair_it != alignment.end(); ++pair_it) { // only annotate experimental peaks with shift - i.e. do not annotated complete loss peaks again @@ -3007,6 +3021,7 @@ static void scoreXLIons_( const double & fragment_intensity = fragment.getIntensity(); // in percent (%) const double & fragment_mz = fragment.getMZ(); const int & fragment_charge = exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX][fragment_index]; + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "fragment_mz:" << fragment_mz << " fragment_charge:" << fragment_charge << endl; #endif @@ -4369,7 +4384,11 @@ static void scoreXLIons_( << "-post-processing-tdc" << "-weights" << weights_out.toQString() << "-nested-xval-bins" << "3"; - //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice + + if (getStringOption_("peptide:enzyme") == "Lys-C") + { + process_params << "-enzyme" << "lys-c"; + } TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); @@ -4846,6 +4865,9 @@ static void scoreXLIons_( std::string s = aas.toUnmodifiedString(); auto last = --s.end(); std::reverse(s.begin(), last); + + // switch cleavage sites (like in Andromeda or DecoyPyrate) + // if (s.size() >= 2) std::swap(s[s.size() - 1], s[s.size() - 2]); e.sequence += s; } @@ -5986,9 +6008,13 @@ static void scoreXLIons_( << "-unitnorm" << "-post-processing-tdc" // << "-nested-xval-bins" << "3" - //<< "-enzyme" << "trypsinp" TODO: make dependent on enzyme choice << "-weights" << weights_out.toQString() << "-out_pin" << pin.toQString(); + + if (getStringOption_("peptide:enzyme") == "Lys-C") + { + process_params << "-enzyme" << "lys-c"; + } // process_params << "-out_pout_target" << "merged_target.tab" << "-out_pout_decoy" << "merged_decoy.tab"; TOPPBase::ExitCodes exit_code = runExternalProcess_(QString("PercolatorAdapter"), process_params); From e03945071356ddac65d968abe465757e31f88881 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Fri, 20 Nov 2020 12:12:45 +0000 Subject: [PATCH 131/471] count and store how often a position in a protein was modified with a specific modification --- .../include/OpenMS/METADATA/ProteinHit.h | 39 ++++++++++++-- src/openms/source/FORMAT/MzTab.cpp | 52 +++++++++++------- src/openms/source/METADATA/ProteinHit.cpp | 4 +- .../source/METADATA/ProteinIdentification.cpp | 54 +++++++++++++++---- 4 files changed, 111 insertions(+), 38 deletions(-) diff --git a/src/openms/include/OpenMS/METADATA/ProteinHit.h b/src/openms/include/OpenMS/METADATA/ProteinHit.h index df1655c4cd6..c0c909a1370 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinHit.h +++ b/src/openms/include/OpenMS/METADATA/ProteinHit.h @@ -47,6 +47,35 @@ namespace OpenMS { + + /** + * @brief Maps a protein position to all observed modifications and associated statistics + * + * For example, to store that position 10 maps to Oxidation (M) which was observed in 123 PSMs. + * + */ + struct OPENMS_DLLAPI ProteinModificationSummary + { + /// basic modification statistic + struct OPENMS_DLLAPI Statistics : public MetaInfoInterface + { + size_t count = 0; + double frequency = 0.0; + }; + + /// compare map + bool operator==(const ProteinModificationSummary& rhs) const + { + return AALevelSummary == rhs.AALevelSummary; + } + + using ModificationsToStatistics = std::map; + using AALevelModificationSummary = std::map; + + /// position -> modification -> statistic (counts, etc.) + AALevelModificationSummary AALevelSummary; + }; + /** @brief Representation of a protein hit @@ -197,11 +226,11 @@ namespace OpenMS /// sets the coverage (in percent) of the protein hit based upon matched peptides void setCoverage(const double coverage); - /// returns the set of modified protein positions - const std::set >& getModifications() const; + /// returns the set of modified protein positions and associated statistics + const ProteinModificationSummary& getModifications() const; - /// sets the set of modified protein positions - void setModifications(std::set >& mods); + /// sets modified protein positions and associated statistics (e.g., counts=PSMs that provided evidance for the modification at this position) + void setModifications(const ProteinModificationSummary& mods); //@} protected: @@ -210,7 +239,7 @@ namespace OpenMS String accession_; ///< the protein identifier String sequence_; ///< the amino acid sequence of the protein hit double coverage_; ///< coverage of the protein based upon the matched peptide sequences - std::set > modifications_; ///< modified positions in a protein + ProteinModificationSummary modifications_; ///< modified positions in a protein }; /// Stream operator diff --git a/src/openms/source/FORMAT/MzTab.cpp b/src/openms/source/FORMAT/MzTab.cpp index 9c34df86115..eb29b2d0f5e 100644 --- a/src/openms/source/FORMAT/MzTab.cpp +++ b/src/openms/source/FORMAT/MzTab.cpp @@ -2288,14 +2288,20 @@ namespace OpenMS // std::map num_peptides_distinct_ms_run; // std::map num_peptides_unique_ms_run; MzTabModificationList modifications; // Modifications identified in the protein. - const std::set>& leader_mods = hit.getModifications(); - for (auto const & m : leader_mods) - { - MzTabModification mztab_mod; - mztab_mod.setModificationIdentifier(MzTab::getModificationIdentifier_(m.second)); - vector > pos; - pos.emplace_back(make_pair(m.first, MzTabParameter())); // position, parameter pair (e.g. FLR) - mztab_mod.setPositionsAndParameters(pos); + const ProteinModificationSummary& leader_mods = hit.getModifications(); + for (auto const & m : leader_mods.AALevelSummary) // for all modified positions + { + size_t position = m.first; // AA position in the protein + const ProteinModificationSummary::ModificationsToStatistics& m2s = m.second; // all modifications -> statistcs + for (auto & modstat : m2s) // for all modifications at current position + { + auto mod = modstat.first; + MzTabModification mztab_mod; + mztab_mod.setModificationIdentifier(MzTab::getModificationIdentifier_(mod)); + vector> pos; + pos.emplace_back(make_pair(position, MzTabParameter())); // position, parameter pair (e.g. FLR) + mztab_mod.setPositionsAndParameters(pos); + } } protein_row.modifications = modifications; @@ -2456,20 +2462,26 @@ namespace OpenMS MzTabParameterList search_engine; // Search engine(s) identifying the protein. protein_row.search_engine = search_engine; + MzTabModificationList modifications; // Modifications identified in the protein. - const std::set>& leader_mods = leader_protein.getModifications(); - for (auto const & m : leader_mods) - { - MzTabModification mztab_mod; - mztab_mod.setModificationIdentifier(MzTab::getModificationIdentifier_(m.second)); - vector > pos; - - // mzTab position is one-based, internal is 0-based so we need to +1 - pos.emplace_back(make_pair(m.first + 1, MzTabParameter())); // position, parameter pair (e.g. FLR) - mztab_mod.setPositionsAndParameters(pos); - vector mztab_mods(1, mztab_mod); - modifications.set(mztab_mods); + const ProteinModificationSummary& leader_mods = leader_protein.getModifications(); + for (auto const & m : leader_mods.AALevelSummary) // for all modified positions + { + size_t position = m.first; // AA position in the protein + const ProteinModificationSummary::ModificationsToStatistics& m2s = m.second; // all modifications -> statistcs + for (auto & modstat : m2s) // for all modifications at current position + { + auto mod = modstat.first; + MzTabModification mztab_mod; + mztab_mod.setModificationIdentifier(MzTab::getModificationIdentifier_(mod)); + vector> pos; + // mzTab position is one-based, internal is 0-based so we need to +1 + pos.emplace_back(make_pair(position + 1, MzTabParameter())); // position, parameter pair (e.g. FLR) + mztab_mod.setPositionsAndParameters(pos); + vector mztab_mods(1, mztab_mod); + modifications.set(mztab_mods); + } } protein_row.modifications = modifications; diff --git a/src/openms/source/METADATA/ProteinHit.cpp b/src/openms/source/METADATA/ProteinHit.cpp index 211fc562750..17f7a32995a 100644 --- a/src/openms/source/METADATA/ProteinHit.cpp +++ b/src/openms/source/METADATA/ProteinHit.cpp @@ -163,12 +163,12 @@ namespace OpenMS coverage_ = coverage; } - const set>& ProteinHit::getModifications() const + const ProteinModificationSummary& ProteinHit::getModifications() const { return modifications_; } - void ProteinHit::setModifications(std::set>& mods) + void ProteinHit::setModifications(const ProteinModificationSummary& mods) { modifications_ = mods; } diff --git a/src/openms/source/METADATA/ProteinIdentification.cpp b/src/openms/source/METADATA/ProteinIdentification.cpp index 40782dc05d9..5b75d5e7423 100644 --- a/src/openms/source/METADATA/ProteinIdentification.cpp +++ b/src/openms/source/METADATA/ProteinIdentification.cpp @@ -685,8 +685,11 @@ namespace OpenMS const std::vector& pep_ids, const StringList& skip_modifications) { - // map protein accession to observed position,modifications pairs - map>> prot2mod; + // map protein accession to observed position -> modifications -> statistics (e.g., counts) + map prot2mod; + + // total count how often evidence for a protein was observed (both unmodified + modified) + map prot2count; for (Size pep_i = 0; pep_i != pep_ids.size(); ++pep_i) { @@ -700,7 +703,16 @@ namespace OpenMS const std::vector& ph_evidences = peptide_hit.getPeptideEvidences(); // skip unmodified peptides - if (aas.isModified() == false) { continue; } + if (aas.isModified() == false) + { + // count unmodified protein + for (Size phe_i = 0; phe_i != ph_evidences.size(); ++phe_i) + { + const String& acc = ph_evidences[phe_i].getProteinAccession(); + prot2count[acc]++; // count protein evidence + } + continue; + } if (aas.isModified()) { @@ -715,7 +727,8 @@ namespace OpenMS { const String& acc = ph_evidences[phe_i].getProteinAccession(); const Size mod_pos = ph_evidences[phe_i].getStart(); // mod at N terminus - prot2mod[acc].insert(make_pair(mod_pos, *res_mod)); + prot2mod[acc].AALevelSummary[mod_pos][*res_mod].count++; // count modified residue in protein + prot2count[acc]++; // count protein evidence } } } @@ -733,7 +746,8 @@ namespace OpenMS { const String& acc = ph_evidences[phe_i].getProteinAccession(); const Size mod_pos = ph_evidences[phe_i].getStart() + ai; // start + ai - prot2mod[acc].insert(make_pair(mod_pos, *res_mod)); + prot2mod[acc].AALevelSummary[mod_pos][*res_mod].count++; // count modified residue in protein + prot2count[acc]++; // count protein evidence } } } @@ -750,7 +764,8 @@ namespace OpenMS { const String& acc = ph_evidences[phe_i].getProteinAccession(); const Size mod_pos = ph_evidences[phe_i].getEnd(); // mod at C terminus - prot2mod[acc].insert(make_pair(mod_pos, *res_mod)); + prot2mod[acc].AALevelSummary[mod_pos][*res_mod].count++; // count modified residue in protein + prot2count[acc]++; // count protein evidence } } } @@ -759,11 +774,28 @@ namespace OpenMS } for (Size i = 0; i < protein_hits_.size(); ++i) - { - const String& accession = protein_hits_[i].getAccession(); - if (prot2mod.find(accession) != prot2mod.end()) - { - protein_hits_[i].setModifications(prot2mod[accession]); + { // for all proteins + const String& acc = protein_hits_[i].getAccession(); + if (prot2mod.find(acc) != prot2mod.end()) + { // if the protein is modified + const size_t total_count = prot2count[acc]; // # modified + unmodified evidences (PSMs) for this protein + + if (total_count == 0) { continue; } + + for (auto& m : prot2mod[acc].AALevelSummary) + { // iterate over all modified positions + ProteinModificationSummary::ModificationsToStatistics& m2ss = m.second; + for (auto & stat : m2ss) + { // iterate over all modifications (key) and statistics (value) at this position + ProteinModificationSummary::Statistics& s = stat.second; + // calculate frequency for this modification at this position as: + // number of PSMs that support that modification at that position divided by + // all PSMs of that protein + s.frequency = static_cast(s.count) / total_count; + } + } + // store modifications and statistics + protein_hits_[i].setModifications(prot2mod[acc]); } } } From 470751204ae743706a07e820b99b17cb16c536e1 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Mon, 23 Nov 2020 13:00:18 +0000 Subject: [PATCH 132/471] move class to new file --- .../include/OpenMS/METADATA/ProteinHit.h | 30 +------- .../METADATA/ProteinModificationSummary.h | 69 +++++++++++++++++++ .../include/OpenMS/METADATA/sources.cmake | 1 + .../METADATA/ProteinModificationSummary.cpp | 42 +++++++++++ src/openms/source/METADATA/sources.cmake | 1 + 5 files changed, 114 insertions(+), 29 deletions(-) create mode 100644 src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h create mode 100644 src/openms/source/METADATA/ProteinModificationSummary.cpp diff --git a/src/openms/include/OpenMS/METADATA/ProteinHit.h b/src/openms/include/OpenMS/METADATA/ProteinHit.h index c0c909a1370..34a9eb92b6e 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinHit.h +++ b/src/openms/include/OpenMS/METADATA/ProteinHit.h @@ -44,38 +44,10 @@ #include #include #include +#include namespace OpenMS { - - /** - * @brief Maps a protein position to all observed modifications and associated statistics - * - * For example, to store that position 10 maps to Oxidation (M) which was observed in 123 PSMs. - * - */ - struct OPENMS_DLLAPI ProteinModificationSummary - { - /// basic modification statistic - struct OPENMS_DLLAPI Statistics : public MetaInfoInterface - { - size_t count = 0; - double frequency = 0.0; - }; - - /// compare map - bool operator==(const ProteinModificationSummary& rhs) const - { - return AALevelSummary == rhs.AALevelSummary; - } - - using ModificationsToStatistics = std::map; - using AALevelModificationSummary = std::map; - - /// position -> modification -> statistic (counts, etc.) - AALevelModificationSummary AALevelSummary; - }; - /** @brief Representation of a protein hit diff --git a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h new file mode 100644 index 00000000000..b87dfbeaf47 --- /dev/null +++ b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h @@ -0,0 +1,69 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2020. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: $ +// -------------------------------------------------------------------------- + +#pragma once + +#include + +#include +#include + +namespace OpenMS +{ + /** + * @brief Maps a protein position to all observed modifications and associated statistics + * + * For example, to store that position 10 maps to Oxidation (M) which was observed in 123 PSMs. + * + */ + struct OPENMS_DLLAPI ProteinModificationSummary + { + /// basic modification statistic + struct OPENMS_DLLAPI Statistics : public MetaInfoInterface + { + size_t count = 0; + double frequency = 0.0; + }; + + /// comparison operator + bool operator==(const ProteinModificationSummary& rhs) const; + + using ModificationsToStatistics = std::map; + using AALevelModificationSummary = std::map; + + /// position -> modification -> statistic (counts, etc.) + AALevelModificationSummary AALevelSummary; + }; + +} diff --git a/src/openms/include/OpenMS/METADATA/sources.cmake b/src/openms/include/OpenMS/METADATA/sources.cmake index 2cf1b51658b..ef7fe02bdfa 100644 --- a/src/openms/include/OpenMS/METADATA/sources.cmake +++ b/src/openms/include/OpenMS/METADATA/sources.cmake @@ -41,6 +41,7 @@ Precursor.h Product.h ProteinHit.h ProteinIdentification.h +ProteinModificationSummary.h Sample.h SampleTreatment.h ScanWindow.h diff --git a/src/openms/source/METADATA/ProteinModificationSummary.cpp b/src/openms/source/METADATA/ProteinModificationSummary.cpp new file mode 100644 index 00000000000..deea4790f61 --- /dev/null +++ b/src/openms/source/METADATA/ProteinModificationSummary.cpp @@ -0,0 +1,42 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2020. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg$ +// -------------------------------------------------------------------------- + +#include + +using namespace OpenMS; + +bool ProteinModificationSummary::operator==(const ProteinModificationSummary& rhs) const +{ + return AALevelSummary == rhs.AALevelSummary; +} diff --git a/src/openms/source/METADATA/sources.cmake b/src/openms/source/METADATA/sources.cmake index 8d89365eeef..13480a013ea 100644 --- a/src/openms/source/METADATA/sources.cmake +++ b/src/openms/source/METADATA/sources.cmake @@ -40,6 +40,7 @@ Precursor.cpp Product.cpp ProteinHit.cpp ProteinIdentification.cpp +ProteinModificationSummary.cpp Sample.cpp SampleTreatment.cpp ScanWindow.cpp From aec695988795c3ebe52cf55e9e32ef49257f4ab2 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 23 Nov 2020 17:33:07 +0100 Subject: [PATCH 133/471] update some test files --- share/OpenMS/CHEMISTRY/unimod.xml | 10887 ++++++++++++---- .../ANALYSIS/RNPXL/RNPxlParameterParsing.cpp | 8 +- .../topp/IDFileConverter_22_output.idXML | 8 +- src/tests/topp/OpenPepXLLF_output.idXML | 46 +- src/tests/topp/OpenPepXLLF_output.mzid | 72 +- src/tests/topp/OpenPepXLLF_output.spec.xml | 1410 +- src/tests/topp/OpenPepXLLF_output.xquest.xml | 12 +- src/tests/topp/SimpleSearchEngine_1_out.idXML | 16 +- 8 files changed, 9342 insertions(+), 3117 deletions(-) diff --git a/share/OpenMS/CHEMISTRY/unimod.xml b/share/OpenMS/CHEMISTRY/unimod.xml index 98f5cc54f04..f6ebd046bba 100644 --- a/share/OpenMS/CHEMISTRY/unimod.xml +++ b/share/OpenMS/CHEMISTRY/unimod.xml @@ -47,12 +47,15 @@ + + + - + + C.-H. Feng, C.-Y. Lu, Analytica Chimica Acta 684 (2011) 80–86 Journal - https://doi.org/10.1016/j.aca.2010.10.042 + http://dx.doi.org/10.1016/j.aca.2010.10.042 @@ -4615,6 +4821,11 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hexnac=1&mode=exact + record_id="143"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hexnac=2&mode=exact + - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&mode=exact + record_id="145"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hexnac=1&mode=exact + - + @@ -4771,6 +4994,11 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=1&mode=exact + - + @@ -4795,6 +5023,11 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hexnac=2&mode=exact + - + - + - + - + - + @@ -4893,6 +5131,11 @@ corrected by subtraction of a further -O at 8.6.2010 Journal + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neuac=1&mode=exact + - + @@ -4917,6 +5160,11 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hexnac=2&mode=exact + - + @@ -4942,6 +5190,11 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?pent=1&hex=1&hexnac=2&mode=exact + - + - + - + @@ -5060,6 +5323,11 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?pent=1&hex=3&hexnac=1&mode=exact + - + @@ -5086,6 +5354,11 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?pent=1&dhex=1&hex=1&hexnac=2&mode=exact + record_id="156"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=1&hexnac=2&mode=exact + - + @@ -5158,6 +5436,11 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?pent=1&hex=2&hexnac=2&mode=exact + - + - + - @@ -5304,6 +5598,11 @@ corrected by subtraction of a further -O at 8.6.2010 Journal + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neuac=2&mode=exact + record_id="161"> spec_group="2"> Selenocysteine conventionally represented by 1 letter code U - + @@ -5430,7 +5734,7 @@ corrected by subtraction of a further -O at 8.6.2010 spec_group="1"/> approved="1" record_id="207"> - + + - + - AA0230 - RESID + NTRY + FindMod @@ -6835,8 +7157,8 @@ corrected by subtraction of a further -O at 8.6.2010 - NTRY - FindMod + AA0230 + RESID @@ -6844,7 +7166,11 @@ corrected by subtraction of a further -O at 8.6.2010 PubMed PMID - Protein which is posttranslationally modified by the attachment of a nitric oxide group on the sulfur atom of one or more cysteine residues. + + X. Zhan, X. Wang, D.M. Desiderio. Mass Spectrom. Rev., 34 (2015), pp. 423-448 + Journal + https://onlinelibrary.wiley.com/doi/epdf/10.1002/mas.21413 + - @@ -6908,11 +7234,6 @@ corrected by subtraction of a further -O at 8.6.2010 Hydroxy ethyl - - 15351294 - PubMed PMID - - J Biol Chem. 1995 Apr 28;270(17):10017-26. Journal @@ -6923,6 +7244,11 @@ corrected by subtraction of a further -O at 8.6.2010 Journal + + 15351294 + PubMed PMID + + 7730303 PubMed PMID @@ -7002,7 +7328,7 @@ corrected by subtraction of a further -O at 8.6.2010 spec_group="1"/> - - + @@ -7609,24 +7941,24 @@ corrected by subtraction of a further -O at 8.6.2010 username_of_poster="whaskins" group_of_poster="users" date_time_posted="2005-04-25 18:20:12" - date_time_modified="2015-05-05 16:10:19" + date_time_modified="2017-06-02 14:24:06" approved="1" record_id="305"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=4&mode=exact + @@ -7701,12 +8038,18 @@ corrected by subtraction of a further -O at 8.6.2010 + Fucosylated biantennary (-1 galactose) + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=4&hexnac=4&mode=exact + @@ -7727,12 +8070,17 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=5&hexnac=4&mode=exact + @@ -7774,12 +8122,17 @@ corrected by subtraction of a further -O at 8.6.2010 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=4&mode=exact + - - record_id="316"> - - spec_group="2"/> record_id="372"> - + - + @@ -10004,6 +10388,11 @@ corrected by subtraction of a further -O at 8.6.2010 RESID + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?phosphate=1&hexnac=1&mode=exact + - + - + @@ -10045,6 +10434,11 @@ corrected by subtraction of a further -O at 8.6.2010 RESID + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?phosphate=1&hex=1&mode=exact + record_id="439"> - - - - - - - - - - Dimethyl pimelimidate Imidoester Cross-linkers Misc. URL - http://www.piercenet.com/files/0668ss5.pdf - - - Hand, E.S., and Jencks, W.P. (1962). Mechanism of the reaction of imidoesters with amines. J. Am. Chem. Soc. 84, 3505-3514. - Journal - - - - Packman, L.C. and Perhan, R.N. (1982). Quaternary Structures the Pyruvate Dehydrogenase Multienzyme Complex of Bacillus StearothermophilusStudies by a New Reversible Crosslinking Procedure with Bis(imidoesters). Biochem. 21, 5171-5175. - Journal - + http://tools.thermofisher.com/content/sfs/manuals/MAN0011314_ImidoesterCrsLnk_DMA_DMP_DMS_DTBP_UG.pdf record_id="477"> - + @@ -10882,22 +11243,28 @@ corrected by subtraction of a further -O at 8.6.2010 - - + - + - + - - + @@ -14620,7 +15041,12 @@ corrected by subtraction of a further -O at 8.6.2010 threo-1,4-dimercaptobutane-2,3-diol - Cleland's reagent + Was DTT_ST + + Proteomics. 2005 Feb;5(2):388-98. Links rnQuantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. + PubMed PMID + 15648052 + Methods Enzymol. 2006;415:113-33. Links rnIdentification of O-GlcNAc sites on proteins.Whelan SA, Hart GW. PubMed PMID @@ -14631,11 +15057,6 @@ corrected by subtraction of a further -O at 8.6.2010 PubMed PMID 12438562 - - Proteomics. 2005 Feb;5(2):388-98. Links rnQuantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. - PubMed PMID - 15648052 - Beta-elimination and Michael addition of dithiothreitol (DTT) to serine and threonine adds a weight of approximately 136.2. m/z values of the TMT® fragment ions to be quantified for 6plex and 10plex: 126.12773 127.12476 128.13443 129.13147 130.14114 131.13818. Additional m/z values for 10plex: 127.13108 128.12811 129.13779 130.13482 - username_of_poster="cparman" group_of_poster="" date_time_posted="2007-03-02 17:24:48" - date_time_modified="2007-03-03 18:28:20" + date_time_modified="2017-10-09 15:48:05" approved="0" record_id="740"> - - spec_group="2"/> - - Cleland's reagent + Was DTT_C:2H(6) + Isotopically labeled Dithiothreitol (DTT) modification of cysteines Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. Proteomics. 2005 5(2):388-98. Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol. Journal @@ -15118,7 +15547,7 @@ corrected by subtraction of a further -O at 8.6.2010 spec_group="1"> Simple cyclic compound C16H16O2 adds to cysteine forming fluorescent derivative. - + @@ -15126,7 +15555,7 @@ corrected by subtraction of a further -O at 8.6.2010 Biochemistry 2005 vol 44 pp 1833-1845 Journal - https://doi.org/10.1021/bi048228c + http://dx.doi.org/10.1021/bi048228c record_id="762"> - username_of_poster="unimod" group_of_poster="" date_time_posted="2008-02-20 14:12:31" - date_time_modified="2009-05-13 18:21:27" + date_time_modified="2018-06-26 15:22:16" approved="0" record_id="827"> @@ -15451,14 +15884,14 @@ corrected by subtraction of a further -O at 8.6.2010 Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181 Journal - https://doi.org/10.1021/pr0255708 + http://dx.doi.org/10.1021/pr0255708 Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP. Nat Biotechnol. 2003 Aug;21(8):921-6 Journal - https://doi.org/10.1038/nbt849 + http://dx.doi.org/10.1038/nbt849 The two glycine residues left on SILAC labeled ubiquitinylated lysine after tryptic digestion @@ -15545,7 +15978,7 @@ Nat Biotechnol. 2003 Aug;21(8):921-6 PLoS ONE 5(11): e14056 Journal - https://doi.org/10.1371/journal.pone.0014056 + http://dx.doi.org/10.1371/journal.pone.0014056 J. Mass. Spectrom. 2007; 42:89-100. Journal - https://doi.org/10.1002/jms.1144 + http://dx.doi.org/10.1002/jms.1144 - - record_id="821"> spec_group="1"/> - Wohlschlegel, J. A. et al., J Proteome Res. 5 761 2006 Journal - https://doi.org/10.1021/pr050451o + http://dx.doi.org/10.1021/pr050451o spec_group="6"> Very low abundance - + @@ -16014,7 +16460,7 @@ Nat Biotechnol. 2003 Aug;21(8):921-6 antiserum and mass spectrometric analysis Misc. URL - https://doi.org/10.1007/s00726-014-1879-8 + http://dx.doi.org/10.1007/s00726-014-1879-8 spec_group="2"> Use when labelling pre-digest - + @@ -16183,7 +16628,7 @@ antiserum and mass spectrometric analysis record_id="890"> - - + Asn-linked glycan from Gram-negative Bacterium + DATDH 12186869 PubMed PMID @@ -16751,7 +17197,7 @@ Efficient incorporation of unsaturated methionine analogues into proteins in viv record_id="911"> Enrichment and site-mapping of O-Linked N-Acetylglucosamine by a combination of chemical/enzymatic tagging, photochemical cleavage, and electron transfer dissociation (ETD) mass spectrometry Journal - https://doi.org/10.1074/mcp.M900268-MCP200 + http://dx.doi.org/10.1074/mcp.M900268-MCP200 + derivatization of Trp residues using the 2,4-dinitrophenyl-sulfenyl chloride (DNPS-Cl) reagent, that leads to a Trp derivative with the DNPS label attached at 2-position of the indole nucleus. - + @@ -17169,11 +17622,11 @@ Efficient incorporation of unsaturated methionine analogues into proteins in viv http://www.piercenet.com/files/1763dh4.pdf - - - - - - @@ -18261,12 +18739,12 @@ Efficient incorporation of unsaturated methionine analogues into proteins in viv http://products.invitrogen.com/ivgn/product/M1602?ICID=search-m1602 - - - - - - - - - - @@ -18872,7 +19381,7 @@ antiserum and mass spectrometric analysis record_id="1044"> @@ -27909,6 +29015,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=4&neuac=1&mode=exact + - + @@ -27935,6 +29046,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=3&hexnac=4&mode=exact + - + @@ -27961,6 +29077,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=4&hexnac=4&pent=1&mode=exact + - + @@ -27989,6 +29110,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=4&hexnac=5&mode=exact + - + @@ -28014,6 +29140,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=7&hexnac=3&mode=exact + - + @@ -28043,6 +29174,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=4&hexnac=3&neuac=1&mode=exact + - + @@ -28069,6 +29205,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=5&hexnac=4&methyl=2&pent=1&mode=exact + - + @@ -28097,6 +29238,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=3&hexnac=6&mode=exact + - + @@ -28125,6 +29271,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=6&hexnac=3&mode=exact + - + @@ -28151,6 +29302,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=4&hexnac=5&mode=exact + - + @@ -28180,6 +29336,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=5&hexa=1&hexnac=3&mode=exact + - + @@ -28208,6 +29369,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?phosphate=1&hex=7&hexnac=3&mode=exact + - + @@ -28234,6 +29400,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=6&hexnac=4&methyl=3&mode=exact + - + @@ -28262,6 +29433,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=2&hex=4&hexnac=4&mode=exact + - + @@ -28288,6 +29464,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=4&hexnac=3&neuac=2&mode=exact + - + @@ -28314,6 +29495,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=4&pent=3&mode=exact + - + @@ -28340,6 +29526,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=5&hexnac=3&pent=1&mode=exact + - + @@ -28368,6 +29559,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=5&hexnac=4&mode=exact + - + @@ -28395,6 +29591,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=4&pent=2&mode=exact + - + @@ -28421,6 +29622,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=5&hexnac=3&neuac=1&mode=exact + - + @@ -28449,6 +29655,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=2&hex=3&hexnac=6&mode=exact + - + @@ -28474,6 +29685,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=9&hexnac=2&mode=exact + record_id="1532"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=4&hexnac=6&mode=exact + - + @@ -28525,32 +29746,43 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=3&hexnac=4&pent=1&mode=exact + - + composition="dHex Hex(5) HexNAc(3) NeuGc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=5&hexnac=3&neugc=1&mode=exact + - + @@ -28577,6 +29809,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=4&hexnac=4&pent=1&mode=exact + record_id="1536"> - @@ -28605,6 +29842,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=4&hexnac=5&mode=exact + record_id="1537"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=7&hexnac=3&mode=exact + - + @@ -28657,6 +29904,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=5&hexnac=4&pent=1&mode=exact + - + @@ -28686,6 +29938,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=2&dhex=1&hex=5&hexa=1&hexnac=3&mode=exact + - + @@ -28711,6 +29968,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=7&mode=exact + - + @@ -28737,6 +29999,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=5&hexnac=4&mode=exact + - + @@ -28766,6 +30033,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=2&hex=4&hexnac=3&neuac=1&mode=exact + - + @@ -28794,6 +30066,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=2&dhex=1&hex=5&hexnac=4&mode=exact + - + @@ -28821,6 +30098,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=5&hexnac=4&methyl=2&pent=1&mode=exact + - + @@ -28847,6 +30129,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=5&hexnac=4&neugc=1&mode=exact + record_id="1546"> - @@ -28875,6 +30162,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=3&hexnac=6&mode=exact + record_id="1547"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=6&hexnac=4&mode=exact + - + @@ -28930,6 +30227,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=5&hexnac=3&neuac=1&mode=exact + - + @@ -28955,6 +30257,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=7&hexnac=4&mode=exact + record_id="1550"> - @@ -28984,6 +30291,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=5&hexnac=3&neugc=1&mode=exact + - + @@ -29010,6 +30322,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=4&hexnac=5&neuac=1&mode=exact + record_id="1552"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=6&hexnac=4&methyl=3&pent=1&mode=exact + - + @@ -29064,6 +30386,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=7&hexnac=3&mode=exact + - + @@ -29092,6 +30419,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?phosphate=1&dhex=1&hex=7&hexnac=3&mode=exact + - + @@ -29118,6 +30450,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=5&hexnac=5&mode=exact + - + @@ -29147,6 +30484,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=4&hexnac=4&neuac=1&mode=exact + - + @@ -29175,6 +30517,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=3&hex=4&hexnac=4&mode=exact + - + @@ -29203,6 +30550,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=3&hexnac=7&mode=exact + - + @@ -29228,6 +30580,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=6&hexnac=5&mode=exact + - + @@ -29256,6 +30613,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=5&hexnac=4&neuac=1&mode=exact + - + @@ -29282,6 +30644,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=6&neuac=1&mode=exact + - + @@ -29308,6 +30675,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=6&mode=exact + - + - + @@ -29345,6 +30717,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neugc=1&mode=exact + - + - + @@ -29382,6 +30759,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=1&mode=exact + - + - - - + + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=1&mode=exact + record_id="1567"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=1&hexnac=1&kdn=1)mode=exact + - + - + @@ -29530,15 +30938,22 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hexnac=2&neuac=1&mode=exact + - - + - + @@ -29602,6 +31021,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=1&methyl=1&mode=exact + - + record_id="1573"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hexnac=2&neugc=1&mode=exact + - + - + - + - + @@ -29787,6 +31231,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexa=1&hexnac=2&mode=exact + - + - + - + @@ -29862,29 +31316,35 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hexnac=3&mode=exact + - - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=1&kdn=1&mode=exact + - + - + @@ -29933,6 +31398,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=3&mode=exact + - + - + - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&mode=exact + record_id="1585"> - @@ -30045,6 +31525,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=2&hexa=1&hexnac=1&mode=exact + - + - + @@ -30079,6 +31564,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexa=1&mode=exact + record_id="1587"> - @@ -30119,6 +31609,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=1&hexnac=2&mode=exact + - + - + @@ -30156,6 +31651,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=1&neuac=1&mode=exact + - + record_id="1590"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=5&mode=exact + record_id="1591"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hexnac=4&mode=exact + - + - + @@ -30297,43 +31810,53 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hexnac=1&neugc=2&mode=exact + - - - - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=1&neugc=1&mode=exact + - + - + @@ -30371,6 +31894,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=1&mode=exact + - + - + @@ -30408,6 +31936,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=1&neugc=1&mode=exact + - + - + @@ -30445,6 +31978,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=1&mode=exact + record_id="1597"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexa=1&hexnac=1&mode=exact + - + - - - + + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=4&hexnac=1&mode=exact + - + - + @@ -30593,6 +32157,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=2&neuac=1&mode=exact + record_id="1602"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=2&neugc=1&mode=exact + - + - + - + record_id="1608"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=3&mode=exact + - + + @@ -30856,6 +32466,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=3&mode=exact + record_id="1611"> - @@ -30896,6 +32511,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=1&hexnac=2&neuac=1&mode=exact + - + - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=4&mode=exact + record_id="1786"> record_id="1614"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hexnac=2&kdn=1&mode=exact + - + - + - + @@ -31075,6 +32715,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hexnac=4&mode=exact + - + - + @@ -31112,12 +32757,18 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neuac=1&neugc=1&mode=exact + - - + - + @@ -31186,6 +32842,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neugc=2&mode=exact + record_id="1620"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?acetyl=1&hex=1&hexnac=1&neuac=2&mode=exact + - + - + @@ -31260,6 +32925,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexa=1&hexnac=1&mode=exact + - + - + - + - + @@ -31378,6 +33058,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=2&neuac=1&mode=exact + record_id="1625"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexa=1&hexnac=1&mode=exact + record_id="1626"> - @@ -31455,41 +33145,62 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=2&hexnac=3&mode=exact + - - - + + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=5&hexnac=1&mode=exact + - + - + @@ -31525,43 +33236,11 @@ antiserum and mass spectrometric analysis - - - - - - - - - - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hexnac=5&mode=exact + record_id="1630"> - + - + @@ -31636,6 +33320,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=2&neugc=1&mode=exact + record_id="1632"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?phosphate=3&hex=5&mode=exact + - + - + - + @@ -31744,6 +33443,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexa=1&hexnac=2&mode=exact + - + - + - + @@ -31821,6 +33530,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=3&neuac=1&mode=exact + - + - + @@ -31858,6 +33572,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=1&hexnac=3&mode=exact + - + - + @@ -31895,6 +33614,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=3&neugc=1&mode=exact + - + - + - + - + @@ -32014,6 +33748,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexa=1&hexnac=3&mode=exact + record_id="1642"> - @@ -32054,6 +33793,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=2&hexnac=2&neuac=1&mode=exact + - + - - + - + @@ -32168,15 +33923,20 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=4&mode=exact + - - + @@ -32204,6 +33975,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=4&mode=exact + - + - + @@ -32241,6 +34017,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=1&neugc=2&mode=exact + - + - + @@ -32278,6 +34059,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=4&hexnac=1&mode=exact + - + - + @@ -32315,6 +34101,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=2&neuac=2&mode=exact + - + - + @@ -32352,6 +34143,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=1&hexnac=2&neuac=1&mode=exact + - + - + - + @@ -32427,43 +34228,54 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hexnac=5&mode=exact + - - - - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=1&hexnac=2&neugc=1&mode=exact + - + - + @@ -32501,12 +34313,17 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=2&hexnac=2&mode=exact + + @@ -32541,6 +34370,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=3&hexnac=3&mode=exact + record_id="1656"> - @@ -32582,80 +34416,107 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=2&dhex=2&hex=2&hexnac=2&mode=exact + - - - - + composition="dHex Hex HexNAc(3) NeuAc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=3&neuac=1&mode=exact + - + - + - + @@ -32729,43 +34595,54 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexa=1&hexnac=2&mode=exact + - - - + composition="dHex Hex HexNAc(3) NeuGc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=3&neugc=1&mode=exact + record_id="1662"> - @@ -32806,6 +34683,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=1&hexnac=2&neuac=2&mode=exact + record_id="1663"> - @@ -32847,6 +34729,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=2&hex=3&hexa=1&hexnac=1&mode=exact + - + - + @@ -32884,6 +34771,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neuac=3&mode=exact + - + - + @@ -32921,6 +34813,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=3&neugc=1&mode=exact + - + - + - + - + record_id="1670"> - @@ -33117,43 +35034,64 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=2&hex=2&hexa=1&hexnac=2&mode=exact + - - + + composition="dHex Hex(2) HexNAc(4)"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=4&mode=exact + record_id="1672"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neugc=3&mode=exact + - + - + record_id="1675"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=2&neuac=2&mode=exact + - + - + - + - + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=2&hex=2&hexnac=3&mode=exact + + + record_id="1680"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hexnac=5&mode=exact + - + - + @@ -33500,44 +35478,54 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=2&neuac=2&mode=exact + - - + composition="dHex(2) Hex(2) HexNAc(2) NeuAc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=2&neuac=1&mode=exact + - + - - + composition="dHex(2) Hex(2) HexNAc(2) NeuGc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=2&neugc=1&mode=exact + record_id="1685"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=5&mode=exact + record_id="1686"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=2&neugc=1&mode=exact + - + - + @@ -33726,6 +35734,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=3&neuac=2&mode=exact + record_id="1688"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=3&neuac=1&mode=exact + - + - + @@ -33800,6 +35818,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=2&hexnac=3&mode=exact + - + - + - + @@ -33873,43 +35901,54 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=4&hexa=1&hexnac=2&mode=exact + - - - + composition="Hex(3) HexNAc(3) NeuAc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=3&neuac=1&mode=exact + - + - + @@ -33947,6 +35986,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexa=2&hexnac=2&mode=exact + record_id="1694"> - @@ -33988,6 +36032,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=2&hexnac=2&neuac=2&mode=exact + - + record_id="1696"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=3&neugc=1&mode=exact + - + - + - + - + - + @@ -34218,6 +36292,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=4&neuac=1&mode=exact + - + - + @@ -34255,6 +36334,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=4&mode=exact + - + record_id="1703"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=4&hexnac=3&kdn=1&mode=exact + - + - + @@ -34370,6 +36464,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=1&neugc=3&mode=exact + - + - + - + - + @@ -34486,6 +36595,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=2&neuac=2&mode=exact + - + record_id="1711"> - @@ -34563,6 +36682,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&hex=3&hexnac=3&neuac=1&mode=exact + record_id="1712"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=2&neuac=2&mode=exact + - + - + - + @@ -34678,44 +36812,54 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=2&neugc=2&mode=exact + - - + composition="dHex(2) Hex(3) HexNAc(2) NeuGc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=2&neugc=1&mode=exact + record_id="1716"> - @@ -34757,6 +36901,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=1&dhex=1&hex=3&hexa=1&hexnac=3&mode=exact + - + - + @@ -34794,6 +36943,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=3&neuac=2&mode=exact + - + - + @@ -34832,6 +36986,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=3&neuac=1&mode=exact + record_id="1719"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=4&hex=2&hexnac=3&mode=exact + - + - + @@ -34907,44 +37071,54 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=3&neuac=1&neugc=1&mode=exact + - - + composition="dHex(2) Hex(2) HexNAc(3) NeuGc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=3&neugc=1&mode=exact + record_id="1722"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=3&hexnac=3&mode=exact + - + - + - + - + @@ -35096,6 +37285,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=3&neugc=2&mode=exact + - + - + - + @@ -35170,6 +37369,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=4&neuac=1&mode=exact + - + - + @@ -35207,6 +37411,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=2&hexnac=4&mode=exact + record_id="1729"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neugc=4&mode=exact + - + - + - - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=2&hexnac=3&kdn=1&mode=exact + - + - + @@ -35395,6 +37625,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=5&mode=exact + - + - + - + - + @@ -35514,44 +37759,54 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=3&neuac=2&mode=exact + - - + composition="dHex(2) Hex(3) HexNAc(3) NeuAc"> + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=3&neuac=1&mode=exact + - + - + @@ -35589,44 +37844,11 @@ antiserum and mass spectrometric analysis - - - - - - - - - - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=4&hex=3&hexnac=3&mode=exact + - + record_id="1743"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hexnac=7&mode=exact + - + - + @@ -35736,6 +37968,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=1&neugc=4&mode=exact + - + - - + @@ -35814,6 +38067,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=5&mode=exact + - + - + @@ -35852,6 +38110,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=2&neugc=3&mode=exact + - + - + - + @@ -35930,6 +38198,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=3&neuac=3&mode=exact + record_id="1750"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=3&neuac=2&mode=exact + - + - + @@ -36006,6 +38284,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=3&hexnac=3&neuac=1&mode=exact + - + - + @@ -36043,6 +38326,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=3&neugc=3&mode=exact + - + record_id="1754"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=4&neuac=2&mode=exact + record_id="1755"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neugc=5&mode=exact + record_id="1756"> - @@ -36195,6 +38498,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?sulfate=2&hex=4&hexnac=4&neuac=1&mode=exact + - + - + - + @@ -36274,6 +38587,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=3&neuac=2&mode=exact + - + record_id="1760"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=2&mode=exact + record_id="1761"> - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=2&mode=exact + record_id="1762"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=3&mode=exact + - + - + - + @@ -36506,6 +38843,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=3&mode=exact + - + - + - + - + @@ -36606,6 +38953,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=2&mode=exact + - + - + - + @@ -36654,6 +39006,16 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hexac=2&mode=exact + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=4&hexnac=2&mode=exact + - + - + - + @@ -36702,6 +39064,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=2&hexnac=3&mode=exact + - + - + - + @@ -36750,7 +39117,12 @@ antiserum and mass spectrometric analysis - + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=3&mode=exact + + record_id="1769"> - + + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=4&hexnac=3&mode=exact + - + - + - + @@ -36845,6 +39222,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=4&hexnac=2&mode=exact + - + - + - + @@ -36893,6 +39275,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=3&mode=exact + - + - + - + @@ -36940,54 +39327,65 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=5&mode=exact + - - - + - + - + @@ -37036,6 +39434,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=3&hexnac=4&mode=exact + - + - + - + @@ -37084,6 +39487,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=5&mode=exact + - + - + - + @@ -37131,6 +39539,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=6&mode=exact + - + - + - + @@ -37179,16 +39592,23 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=4&hexnac=4&neuac=1&mode=exact + - - - + - + - + @@ -37274,6 +39698,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=6&hexnac=4&mode=exact + - + - + - + @@ -37321,6 +39750,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?hex=5&hexnac=5&mode=exact + - + - + - + @@ -37369,54 +39803,65 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=6&mode=exact + - - - + - + - + @@ -37465,6 +39910,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=3&hex=4&hexnac=4&mode=exact + - + - + - + @@ -37513,6 +39963,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=5&neuac=1&mode=exact + - + - + - + @@ -37561,6 +40016,11 @@ antiserum and mass spectrometric analysis + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=4&hexnac=5&mode=exact + PubMed PMID http://www.ncbi.nlm.nih.gov/pubmed/23924801 + + Composition search GlyConnect + Misc. URL + https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=7&hexnac=4&mode=exact + - - record_id="1837"> + + + + + + + + + + + + Photo-cross-linking and high-resolution mass spectrometry for assignment of RNRNA-binding sites in RNRNA-binding proteins + Journal + http://dx.doi.org/10.1038/nmeth.3092 + + - - - @@ -38716,5 +44936,14 @@ derivative" spec_group="5"/> + + + + + + + + + diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp index 6ece8c5ac83..bcfba3b707e 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp @@ -193,21 +193,21 @@ RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(StringList fragment_ // register all fragment adducts as N- and C-terminal modification (if not already registered) if (!ModificationsDB::getInstance()->has(name)) { - ResidueModification * c_term = new ResidueModification(); + std::unique_ptr c_term{new ResidueModification()}; c_term->setId(name); c_term->setName(name); c_term->setFullId(name + " (C-term)"); c_term->setTermSpecificity(ResidueModification::C_TERM); c_term->setDiffMonoMass(fad.mass); - ModificationsDB::getInstance()->addModification(c_term); + ModificationsDB::getInstance()->addModification(std::move(c_term)); - ResidueModification * n_term = new ResidueModification(); + std::unique_ptr n_term{new ResidueModification()}; n_term->setId(name); n_term->setName(name); n_term->setFullId(name + " (N-term)"); n_term->setTermSpecificity(ResidueModification::N_TERM); n_term->setDiffMonoMass(fad.mass); - ModificationsDB::getInstance()->addModification(n_term); + ModificationsDB::getInstance()->addModification(std::move(n_term)); } } diff --git a/src/tests/topp/IDFileConverter_22_output.idXML b/src/tests/topp/IDFileConverter_22_output.idXML index a89f35a395b..33eb5567401 100644 --- a/src/tests/topp/IDFileConverter_22_output.idXML +++ b/src/tests/topp/IDFileConverter_22_output.idXML @@ -18,7 +18,7 @@ - + @@ -44,7 +44,7 @@ - + @@ -77,7 +77,7 @@ - + @@ -110,7 +110,7 @@ - + diff --git a/src/tests/topp/OpenPepXLLF_output.idXML b/src/tests/topp/OpenPepXLLF_output.idXML index 3082e7e22ab..5fb7f918512 100644 --- a/src/tests/topp/OpenPepXLLF_output.idXML +++ b/src/tests/topp/OpenPepXLLF_output.idXML @@ -1,10 +1,10 @@ - + - + @@ -24,7 +24,7 @@ - + @@ -48,16 +48,16 @@ - + - - - + + + @@ -166,16 +166,16 @@ - + - - - + + + @@ -284,16 +284,16 @@ - + - - - + + + @@ -343,16 +343,16 @@ - + - - - + + + @@ -402,16 +402,16 @@ - + - - - + + + diff --git a/src/tests/topp/OpenPepXLLF_output.mzid b/src/tests/topp/OpenPepXLLF_output.mzid index ada3c335a2c..f2443fae96b 100644 --- a/src/tests/topp/OpenPepXLLF_output.mzid +++ b/src/tests/topp/OpenPepXLLF_output.mzid @@ -4,7 +4,7 @@ xmlns="http://psidev.info/psi/pi/mzIdentML/1.2" version="1.2.0" id="OpenMS_17447818880105247092" - creationDate="2020-10-31T22:11:37"> + creationDate="2020-11-23T17:31:49"> @@ -12,12 +12,12 @@ - + - + @@ -27,7 +27,7 @@ - + LPDPVKEYGCAPWPMVEKLIK @@ -46,19 +46,19 @@ - + KKSNSISVGEFYRDAVLQR - + IVEGLKFPNEFDELEIQGK - + VEPSWLGPLFPDKTSNLR @@ -79,7 +79,7 @@ - + LPDPVKEYGCAPWPMVEKLIK @@ -98,7 +98,7 @@ - + @@ -111,7 +111,7 @@ - + @@ -161,12 +161,12 @@ - + - + @@ -214,16 +214,16 @@ - + - - - + + + @@ -359,16 +359,16 @@ - + - - - + + + @@ -490,16 +490,16 @@ - + - - - + + + @@ -566,16 +566,16 @@ - + - - - + + + @@ -629,16 +629,16 @@ - + - - - + + + @@ -681,16 +681,16 @@ - + - - - + + + diff --git a/src/tests/topp/OpenPepXLLF_output.spec.xml b/src/tests/topp/OpenPepXLLF_output.spec.xml index 61c251c4755..297332d4121 100644 --- a/src/tests/topp/OpenPepXLLF_output.spec.xml +++ b/src/tests/topp/OpenPepXLLF_output.spec.xml @@ -462,7 +462,7 @@ OTgzODg2NzAwMDE0NAkwLjM5MDEyNQkwCjExMDcuNjYyNzE5NzI2OTk5OTY3CTAuMDc3MDE4CTAK MTEwOC45MDI5NTQxMDE5OTk5NjcJMC40NjcwMzgJMAoxMTA5LjU1MjI0NjA5NDAwMDExMQkxLjAJ 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+1,13 @@ -<<<<<<< HEAD -======= - ->>>>>>> upstream/develop + + -<<<<<<< HEAD - -======= - ->>>>>>> upstream/develop + @@ -28,14 +22,14 @@ - + - + From d60d5374477000bae4ec0a8f7726824e60577346 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Tue, 24 Nov 2020 09:28:53 +0000 Subject: [PATCH 134/471] add mutable access --- src/openms/include/OpenMS/METADATA/ProteinHit.h | 3 +++ src/openms/source/METADATA/ProteinHit.cpp | 5 +++++ 2 files changed, 8 insertions(+) diff --git a/src/openms/include/OpenMS/METADATA/ProteinHit.h b/src/openms/include/OpenMS/METADATA/ProteinHit.h index 34a9eb92b6e..9c369b7467a 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinHit.h +++ b/src/openms/include/OpenMS/METADATA/ProteinHit.h @@ -201,6 +201,9 @@ namespace OpenMS /// returns the set of modified protein positions and associated statistics const ProteinModificationSummary& getModifications() const; + /// returns the mutable set of modified protein positions and associated statistics + ProteinModificationSummary& getModifications(); + /// sets modified protein positions and associated statistics (e.g., counts=PSMs that provided evidance for the modification at this position) void setModifications(const ProteinModificationSummary& mods); //@} diff --git a/src/openms/source/METADATA/ProteinHit.cpp b/src/openms/source/METADATA/ProteinHit.cpp index 17f7a32995a..69960db45dc 100644 --- a/src/openms/source/METADATA/ProteinHit.cpp +++ b/src/openms/source/METADATA/ProteinHit.cpp @@ -168,6 +168,11 @@ namespace OpenMS return modifications_; } + ProteinModificationSummary& ProteinHit::getModifications() + { + return modifications_; + } + void ProteinHit::setModifications(const ProteinModificationSummary& mods) { modifications_ = mods; From d1771c4702caf2672a22afaef4beff9b225a9b9e Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Tue, 24 Nov 2020 13:54:21 +0000 Subject: [PATCH 135/471] removed meta info interface --- .../include/OpenMS/METADATA/ProteinModificationSummary.h | 7 +++---- src/openms/source/FORMAT/MzTab.cpp | 4 ++-- src/openms/source/METADATA/ProteinIdentification.cpp | 6 +++--- src/openms/source/METADATA/ProteinModificationSummary.cpp | 5 +++++ 4 files changed, 13 insertions(+), 9 deletions(-) diff --git a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h index b87dfbeaf47..24e8df7eba1 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h +++ b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h @@ -35,8 +35,6 @@ #pragma once #include - -#include #include namespace OpenMS @@ -50,8 +48,9 @@ namespace OpenMS struct OPENMS_DLLAPI ProteinModificationSummary { /// basic modification statistic - struct OPENMS_DLLAPI Statistics : public MetaInfoInterface + struct OPENMS_DLLAPI Statistics { + bool operator==(const Statistics& rhs) const; size_t count = 0; double frequency = 0.0; }; @@ -59,7 +58,7 @@ namespace OpenMS /// comparison operator bool operator==(const ProteinModificationSummary& rhs) const; - using ModificationsToStatistics = std::map; + using ModificationsToStatistics = std::map; using AALevelModificationSummary = std::map; /// position -> modification -> statistic (counts, etc.) diff --git a/src/openms/source/FORMAT/MzTab.cpp b/src/openms/source/FORMAT/MzTab.cpp index eb29b2d0f5e..1bf616b45aa 100644 --- a/src/openms/source/FORMAT/MzTab.cpp +++ b/src/openms/source/FORMAT/MzTab.cpp @@ -2297,7 +2297,7 @@ namespace OpenMS { auto mod = modstat.first; MzTabModification mztab_mod; - mztab_mod.setModificationIdentifier(MzTab::getModificationIdentifier_(mod)); + mztab_mod.setModificationIdentifier(MzTab::getModificationIdentifier_(*mod)); vector> pos; pos.emplace_back(make_pair(position, MzTabParameter())); // position, parameter pair (e.g. FLR) mztab_mod.setPositionsAndParameters(pos); @@ -2474,7 +2474,7 @@ namespace OpenMS { auto mod = modstat.first; MzTabModification mztab_mod; - mztab_mod.setModificationIdentifier(MzTab::getModificationIdentifier_(mod)); + mztab_mod.setModificationIdentifier(MzTab::getModificationIdentifier_(*mod)); vector> pos; // mzTab position is one-based, internal is 0-based so we need to +1 pos.emplace_back(make_pair(position + 1, MzTabParameter())); // position, parameter pair (e.g. FLR) diff --git a/src/openms/source/METADATA/ProteinIdentification.cpp b/src/openms/source/METADATA/ProteinIdentification.cpp index 5b75d5e7423..9714f0ddabc 100644 --- a/src/openms/source/METADATA/ProteinIdentification.cpp +++ b/src/openms/source/METADATA/ProteinIdentification.cpp @@ -727,7 +727,7 @@ namespace OpenMS { const String& acc = ph_evidences[phe_i].getProteinAccession(); const Size mod_pos = ph_evidences[phe_i].getStart(); // mod at N terminus - prot2mod[acc].AALevelSummary[mod_pos][*res_mod].count++; // count modified residue in protein + prot2mod[acc].AALevelSummary[mod_pos][res_mod].count++; // count modified residue in protein prot2count[acc]++; // count protein evidence } } @@ -746,7 +746,7 @@ namespace OpenMS { const String& acc = ph_evidences[phe_i].getProteinAccession(); const Size mod_pos = ph_evidences[phe_i].getStart() + ai; // start + ai - prot2mod[acc].AALevelSummary[mod_pos][*res_mod].count++; // count modified residue in protein + prot2mod[acc].AALevelSummary[mod_pos][res_mod].count++; // count modified residue in protein prot2count[acc]++; // count protein evidence } } @@ -764,7 +764,7 @@ namespace OpenMS { const String& acc = ph_evidences[phe_i].getProteinAccession(); const Size mod_pos = ph_evidences[phe_i].getEnd(); // mod at C terminus - prot2mod[acc].AALevelSummary[mod_pos][*res_mod].count++; // count modified residue in protein + prot2mod[acc].AALevelSummary[mod_pos][res_mod].count++; // count modified residue in protein prot2count[acc]++; // count protein evidence } } diff --git a/src/openms/source/METADATA/ProteinModificationSummary.cpp b/src/openms/source/METADATA/ProteinModificationSummary.cpp index deea4790f61..e75fef074a6 100644 --- a/src/openms/source/METADATA/ProteinModificationSummary.cpp +++ b/src/openms/source/METADATA/ProteinModificationSummary.cpp @@ -40,3 +40,8 @@ bool ProteinModificationSummary::operator==(const ProteinModificationSummary& rh { return AALevelSummary == rhs.AALevelSummary; } + +bool ProteinModificationSummary::Statistics::operator==(const Statistics& rhs) const +{ + return std::tie(count, frequency) == std::tie(rhs.count, rhs.frequency); +} From 5b786a991d2ab630cd025911e52c3cb3b66bc970 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Tue, 24 Nov 2020 15:35:38 +0000 Subject: [PATCH 136/471] add false localization rate as statistic --- .../include/OpenMS/METADATA/ProteinModificationSummary.h | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h index 24e8df7eba1..d9959a68b64 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h +++ b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h @@ -51,8 +51,9 @@ namespace OpenMS struct OPENMS_DLLAPI Statistics { bool operator==(const Statistics& rhs) const; - size_t count = 0; - double frequency = 0.0; + size_t count = 0; /// total number of PSMs supporting the modification at this position + double frequency = 0.0; /// PSMs with modification / total number of PSMs + double FLR = 0.0; /// false localization rate }; /// comparison operator From bda363a5edf405f429623c9902ba96ff3b89a84b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 24 Nov 2020 19:14:07 +0100 Subject: [PATCH 137/471] output protein statistics --- src/tests/topp/CMakeLists.txt | 10 +- src/tests/topp/OpenNuXL_1_parameters.ini | 74 ++++--- src/utils/OpenNuXL.cpp | 262 ++++++++++++++++++++--- 3 files changed, 285 insertions(+), 61 deletions(-) diff --git a/src/tests/topp/CMakeLists.txt b/src/tests/topp/CMakeLists.txt index b1d12a0968d..13ef999bd88 100644 --- a/src/tests/topp/CMakeLists.txt +++ b/src/tests/topp/CMakeLists.txt @@ -1894,13 +1894,13 @@ endif() #------------------------------------------------------------------------------ # OpenNuXL add_test("TOPP_OpenNuXL_1" ${TOPP_BIN_PATH}/OpenNuXL -test -in -${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_1_output.tmp -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini) +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_1_output.tmp -RNPxl:decoys "false" -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini) add_test("TOPP_OpenNuXL_1_out1" ${DIFF} -whitelist "IdentificationRun date" "db=" -in1 OpenNuXL_1_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_1_output.idXML ) set_tests_properties("TOPP_OpenNuXL_1_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_1") # test internal decoy generation add_test("TOPP_OpenNuXL_2" ${TOPP_BIN_PATH}/OpenNuXL -test -in -${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_2_output.tmp -RNPxl:decoys -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini) +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_2_output.tmp -RNPxl:decoys "true" -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini) add_test("TOPP_OpenNuXL_2_out1" ${DIFF} -whitelist "IdentificationRun date" "db=" -in1 OpenNuXL_2_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_2_output.idXML ) set_tests_properties("TOPP_OpenNuXL_2_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_2") @@ -1916,7 +1916,7 @@ set_tests_properties("TOPP_OpenNuXL_3_out2" PROPERTIES DEPENDS "TOPP_OpenNuXL_3" # reporting of multiple hits and tsv output and decoy generation add_test("TOPP_OpenNuXL_4" ${TOPP_BIN_PATH}/OpenNuXL -test -in -${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -RNPxl:decoys -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_4_output.tmp -report:top_hits 2 -out_tsv OpenNuXL_4_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast) +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -RNPxl:decoys "true" -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_4_output.tmp -report:top_hits 2 -out_tsv OpenNuXL_4_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast) add_test("TOPP_OpenNuXL_4_out1" ${DIFF} -whitelist "IdentificationRun date" "db=" -in1 OpenNuXL_4_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_4_output.idXML ) add_test("TOPP_OpenNuXL_4_out2" ${DIFF} -in1 OpenNuXL_4_output2.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_4_output2.tsv ) @@ -1925,14 +1925,14 @@ set_tests_properties("TOPP_OpenNuXL_4_out2" PROPERTIES DEPENDS "TOPP_OpenNuXL_4" # test internal decoy generation - slow scoring add_test("TOPP_OpenNuXL_5" ${TOPP_BIN_PATH}/OpenNuXL -test -in -${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_5_output.tmp -RNPxl:decoys -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini -RNPxl:scoring slow) +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_5_output.tmp -RNPxl:decoys "true" -ini ${DATA_DIR_TOPP}/OpenNuXL_1_parameters.ini -RNPxl:scoring slow) add_test("TOPP_OpenNuXL_5_out1" ${DIFF} -whitelist "IdentificationRun date" "db=" -in1 OpenNuXL_5_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_5_output.idXML ) set_tests_properties("TOPP_OpenNuXL_5_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_5") # reporting of multiple hits and tsv output and decoy generation with huge mass window so that all candidates are scored add_test("TOPP_OpenNuXL_6" ${TOPP_BIN_PATH}/OpenNuXL -test -in -${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -RNPxl:decoys -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_6_output.tmp -report:top_hits 2 -out_tsv OpenNuXL_6_output2.tmp -precursor:mass_tolerance 1e9 -RNPxl:scoring slow) +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -RNPxl:decoys "true" -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_6_output.tmp -report:top_hits 2 -out_tsv OpenNuXL_6_output2.tmp -precursor:mass_tolerance 1e9 -RNPxl:scoring slow) add_test("TOPP_OpenNuXL_6_out1" ${DIFF} -whitelist "IdentificationRun date" "db=" -in1 OpenNuXL_6_output.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_6_output.idXML ) add_test("TOPP_OpenNuXL_6_out2" ${DIFF} -in1 OpenNuXL_6_output2.tmp -in2 ${DATA_DIR_TOPP}/OpenNuXL_6_output2.tsv ) diff --git a/src/tests/topp/OpenNuXL_1_parameters.ini b/src/tests/topp/OpenNuXL_1_parameters.ini index f0ba4ca495b..a721b178a42 100644 --- a/src/tests/topp/OpenNuXL_1_parameters.ini +++ b/src/tests/topp/OpenNuXL_1_parameters.ini @@ -1,65 +1,82 @@ - - - + + + - + + + - + + + + + + + + + - - - + + + - + - + - - + + - + - + - + + - + + + + + - - - + + + - + + + - - + + @@ -68,16 +85,19 @@ - + - - - - + + + + + + + diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index f508d9434d8..d2e1823ddc9 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -409,8 +409,9 @@ class AnnotatedHit float sequence_score = 0; float best_localization_score = 0; - String localization_scores; - String best_localization; + String localization_scores = 0; + String best_localization; + int best_localization_position = -1; // UNKNOWN std::vector fragment_annotations; size_t tag_unshifted = 0; @@ -600,7 +601,8 @@ class OpenNuXL : registerStringOption_("RNPxl:scoring", "", "fast", "Scoring algorithm used in prescoring (fast: total-loss, slow: all losses).", false, false); setValidStrings_("RNPxl:scoring", {"fast", "slow"}); - registerFlag_("RNPxl:decoys", "Generate decoy sequences and spectra."); + registerStringOption_("RNPxl:decoys", "", "true", "Generate decoys internally (recommended).", false, false); + setValidStrings_("RNPxl:decoys", {"true", "false"}); registerFlag_("RNPxl:CysteineAdduct", "Use this flag if the +152 adduct is expected.", true); registerFlag_("RNPxl:filter_fractional_mass", "Use this flag to filter non-crosslinks by fractional mass.", true); @@ -3243,6 +3245,7 @@ static void scoreXLIons_( #endif String best_localization = unmodified_sequence; + int best_localization_position = -1; // UNKNOWN double best_localization_score = 0; String localization_scores; for (Size i = 0; i != sites_sum_score.size(); ++i) @@ -3269,6 +3272,7 @@ static void scoreXLIons_( if (best_localization_score > 0.0 && sites_sum_score[i] >= best_localization_score - 1e-6) { best_localization[i] = tolower(best_localization[i]); + best_localization_position = i; // Note: check if there are situations where multiple have the same score } } #ifdef DEBUG_OpenNuXL @@ -3288,6 +3292,7 @@ static void scoreXLIons_( a.localization_scores = localization_scores; a.best_localization = best_localization; a.best_localization_score = best_localization_score; + a.best_localization_position = best_localization_position; a.fragment_annotations = fas; #ifdef DEBUG_OpenNuXL @@ -3474,21 +3479,22 @@ static void scoreXLIons_( ph.setMetaValue(String("NuXL:NA_length"), NA_length); } - ph.setMetaValue(String("NuXL:NT"), String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide - ph.setMetaValue(String("NuXL:NA_MASS_z0"), na_mass_z0); // NA uncharged mass via empirical formula - ph.setMetaValue(String("NuXL:isXL"), na_mass_z0 > 0); - ph.setMetaValue(String("NuXL:isPhospho"), is_phospho); + ph.setMetaValue("NuXL:NT", String(ah.cross_linked_nucleotide)); // the cross-linked nucleotide + ph.setMetaValue("NuXL:NA_MASS_z0", na_mass_z0); // NA uncharged mass via empirical formula + ph.setMetaValue("NuXL:isXL", na_mass_z0 > 0); + ph.setMetaValue("NuXL:isPhospho", is_phospho); - ph.setMetaValue(String("NuXL:best_localization_score"), ah.best_localization_score); + ph.setMetaValue("NuXL:best_localization_score", ah.best_localization_score); if (!ah.localization_scores.empty()) { - ph.setMetaValue(String("NuXL:localization_scores"), ah.localization_scores); + ph.setMetaValue("NuXL:localization_scores", ah.localization_scores); } else { - ph.setMetaValue(String("NuXL:localization_scores"), "NA"); + ph.setMetaValue("NuXL:localization_scores", "NA"); } - ph.setMetaValue(String("NuXL:best_localization"), ah.best_localization); + ph.setMetaValue("NuXL:best_localization", ah.best_localization); + ph.setMetaValue("NuXL:best_localization_position", ah.best_localization_position); // one-hot encoding of cross-linked nucleotide const String can_cross_link = getStringOption_("RNPxl:can_cross_link"); @@ -4267,6 +4273,179 @@ static void scoreXLIons_( return EXECUTION_OK; } + void annotateProteinModificationForTopHits_(vector& prot_ids, const vector& peps, TextFile& tsv_file) + { + assert(prots.size() == 1); // support for one run only + + ProteinIdentification& prot_id = prot_ids[0]; + vector& proteins = prot_id.getHits(); + + // create a user defined modification + ResidueModification* xl = new ResidueModification(); + xl->setFullId("x"); // something not used in ResidueDB + xl->setOrigin('X'); // any AA + + // create lookup accession -> protein + map acc2protein_targets; + map acc2protein_decoys; + for (ProteinHit& protein : proteins) + { + if (protein.getMetaValue("target_decoy").toString().hasPrefix("target")) + { + acc2protein_targets[protein.getAccession()] = &protein; + } + else + { + acc2protein_decoys[protein.getAccession()] = &protein; + } + } + + // store modification statistic for every protein + for (const PeptideIdentification& pep : peps) + { + auto& hits = pep.getHits(); + for (const PeptideHit& ph : hits) + { + const std::vector& ph_evidences = ph.getPeptideEvidences(); + const int best_localization = ph.getMetaValue("NuXL:best_localization_position"); + for (auto& ph_evidence : ph_evidences) + { + const String& acc = ph_evidence.getProteinAccession(); + const int peptide_start_in_protein = ph_evidence.getStart(); + + if (peptide_start_in_protein < 0 || best_localization < 0) continue; + + const int xl_pos_in_protein = peptide_start_in_protein + best_localization; + + bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + + // retrieve protein the evidence points to + ProteinHit* protein = is_target ? acc2protein_targets[acc] : acc2protein_decoys[acc]; + if (xl_pos_in_protein < protein->getSequence().size()) + { + auto mods = protein->getModifications(); // TODO: add mutable reference access + mods.AALevelSummary[xl_pos_in_protein][*xl].count++; + protein->setModifications(mods); + } + } + } + } + + map aa2protein_count_targets; // how many proteins have that AA cross-linked + map aa2psm_count_targets; // how many PSMs have that AA cross-linked + map aa2protein_count_decoys; // how many proteins have that AA cross-linked + map aa2psm_count_decoys; // how many PSMs have that AA cross-linked + + for (const ProteinIdentification& prot_id : prot_ids) + { + const vector& proteins = prot_id.getHits(); + for (const ProteinHit& protein : proteins) + { + const String& seq = protein.getSequence(); + const String& acc = protein.getAccession(); + bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + auto mods = protein.getModifications(); + + tsv_file.addLine(acc); + + // count how many PSMs support XL-ed position in a protein + map position2psm_count; + for (const auto& p2ms : mods.AALevelSummary) + { + size_t position = p2ms.first; + for (const auto& m2s : p2ms.second) + { + const auto stat = m2s.second; + position2psm_count[position] += stat.count; + } + } + + // put string with AA, position, PSM count in sequence: e.g.: [Y123,2] + String annotated_sequence; + size_t p{0}; + for (const auto p2psm : position2psm_count) + { + while (p < p2psm.first) { annotated_sequence += seq[p]; ++p; } + annotated_sequence += "[" + String(p2psm.first + 1) + "," + String(p2psm.second) + "]"; + } + tsv_file.addLine(annotated_sequence); + + set already_counted_at_protein_level; + for (const auto& p2ms : mods.AALevelSummary) + { + size_t position = p2ms.first; + + // retrieve AA a xl position + char AA_at_position = '?'; + if (seq.size() > position) + { + AA_at_position = seq[position]; + } + + // count a modified AA only once per protein for protein count + if (already_counted_at_protein_level.count(AA_at_position) == 0) + { + if (is_target) + { + aa2protein_count_targets[AA_at_position]++; + } + else + { + aa2protein_count_decoys[AA_at_position]++; + } + already_counted_at_protein_level.insert(AA_at_position); + } + + for (const auto& m2s : p2ms.second) + { + auto stat = m2s.second; + size_t count = stat.count; + if (is_target) + { + aa2psm_count_targets[AA_at_position] += count; + } + else + { + aa2psm_count_decoys[AA_at_position] += count; + } + tsv_file.addLine(m2s.first.getFullId() + ":" + AA_at_position + String(position) + "(" + String(count) + ")"); + } + } + } + } + + tsv_file.addLine("============================================================="); + tsv_file.addLine("Protein summary for decoy proteins:"); + tsv_file.addLine("AA:proteins"); + for (const auto& a2p : aa2protein_count_decoys) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + } + + tsv_file.addLine("============================================================="); + tsv_file.addLine("PSM summary for decoy PSMs:"); + tsv_file.addLine("AA:PSMs"); + for (const auto& a2p : aa2psm_count_decoys) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + } + tsv_file.addLine("============================================================="); + tsv_file.addLine("Protein summary for target proteins:"); + tsv_file.addLine("AA:proteins"); + for (const auto& a2p : aa2protein_count_targets) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + } + + tsv_file.addLine("============================================================="); + tsv_file.addLine("PSM summary for target PSMs:"); + tsv_file.addLine("AA:PSMs"); + for (const auto& a2p : aa2psm_count_targets) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + } + } + ExitCodes main_(int, const char**) override { ProgressLogger progresslogger; @@ -4294,7 +4473,7 @@ static void scoreXLIons_( Int max_precursor_charge = getIntOption_("precursor:max_charge"); double precursor_mass_tolerance = getDoubleOption_("precursor:mass_tolerance"); double fragment_mass_tolerance = getDoubleOption_("fragment:mass_tolerance"); - bool generate_decoys = getFlag_("RNPxl:decoys"); + bool generate_decoys = getStringOption_("RNPxl:decoys") == "true"; StringList filter = getStringList_("filter"); bool filter_pc_mass_error = find(filter.begin(), filter.end(), "filter_pc_mass_error") != filter.end(); @@ -4379,11 +4558,11 @@ static void scoreXLIons_( process_params << "-in" << out_idxml.toQString() << "-out" << perc_out.toQString() << "-percolator_executable" << percolator_executable.toQString() - << "-train-best-positive" + << "-train_best_positive" << "-score_type" << "q-value" - << "-post-processing-tdc" + << "-post_processing_tdc" << "-weights" << weights_out.toQString() - << "-nested-xval-bins" << "3"; + << "-nested_xval_bins" << "3"; if (getStringOption_("peptide:enzyme") == "Lys-C") { @@ -4669,6 +4848,7 @@ static void scoreXLIons_( // calculate FDR FalseDiscoveryRate fdr; Param p = fdr.getParameters(); + p.setValue("add_decoy_proteins", "true"); // we still want decoys in the result (e.g., to run percolator) p.setValue("add_decoy_peptides", "true"); // we still want decoys in the result (e.g., to run percolator) if (report_top_hits >= 2) { @@ -4800,8 +4980,10 @@ static void scoreXLIons_( progresslogger.startProgress(0, 1, "Calculate Nucleotide Tags..."); calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); + progresslogger.endProgress(); // build multimap of precursor mass to scan index (and perform some mass and length based filtering) + progresslogger.startProgress(0, 1, "Mapping precursors to scan..."); using MassToScanMultiMap = multimap>; MassToScanMultiMap multimap_mass_2_scan_index; // map precursor mass to scan index and (potential) isotopic missassignment mapPrecursorMassesToScans(min_precursor_charge, @@ -4811,6 +4993,7 @@ static void scoreXLIons_( peptide_min_size, spectra, multimap_mass_2_scan_index); + progresslogger.endProgress(); // preallocate storage for PSMs vector nr_candidates(spectra.size(), 0); @@ -4844,10 +5027,10 @@ static void scoreXLIons_( // generate decoy protein sequences by reversing them if (generate_decoys) { + progresslogger.startProgress(0, 1, "Generating decoys..."); ProteaseDigestion digestor; digestor.setEnzyme(getStringOption_("peptide:enzyme")); digestor.setMissedCleavages(0); // for decoy generation disable missed cleavages - progresslogger.startProgress(0, 1, "Generate decoys..."); // append decoy proteins const size_t old_size = fasta_db.size(); @@ -5465,7 +5648,7 @@ static void scoreXLIons_( vector peptide_ids; vector protein_ids; - progresslogger.startProgress(0, 1, "Post-processing PSMs..."); + progresslogger.startProgress(0, 1, "Post-processing PSMs... (spectra filtering)"); /////////////////////////////////////////////////////////////////////////////////////////////////// // Localization @@ -5483,9 +5666,9 @@ static void scoreXLIons_( true, window_size, peak_count); // annotate charge (true) calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); - progresslogger.startProgress(0, 1, "localization..."); - + progresslogger.endProgress(); + progresslogger.startProgress(0, 1, "Post-processing PSMs... (localization of cross-links)"); assert(spectra.size() == annotated_XLs.size()); assert(spectra.size() == annotated_peptides.size()); @@ -5504,8 +5687,9 @@ static void scoreXLIons_( fragment_mass_tolerance_unit_ppm, all_feasible_fragment_adducts); - progresslogger.startProgress(0, 1, "Post-processing and annotation..."); + progresslogger.endProgress(); + progresslogger.startProgress(0, 1, "Post-processing PSMs... (annotation)"); // remove all but top n scoring PSMs again // Note: this is currently necessary as postScoreHits_ might reintroduce nucleotide specific hits for fast scoring filterTopNAnnotations_(annotated_XLs, report_top_hits); @@ -5522,6 +5706,7 @@ static void scoreXLIons_( max_variable_mods_per_peptide, purities, nr_candidates); + progresslogger.endProgress(); protein_ids[0].setPrimaryMSRunPath({"file://" + File::basename(in_mzml)}); @@ -5533,6 +5718,8 @@ static void scoreXLIons_( param_pi.setValue("enzyme:name", getStringOption_("peptide:enzyme")); param_pi.setValue("enzyme:specificity", "full"); param_pi.setValue("missing_decoy_action", "silent"); + param_pi.setValue("write_protein_sequence", "true"); + param_pi.setValue("write_protein_description", "true"); indexer.setParameters(param_pi); PeptideIndexing::ExitCodes indexer_exit = indexer.run(fasta_db, protein_ids, peptide_ids); @@ -5592,16 +5779,10 @@ static void scoreXLIons_( ph.setMetaValue("NuXL:QQ_TIC", QQ_TIC[scan_index].quantileOfValue(ph.getMetaValue("NuXL:total_MIC"))); ph.setMetaValue("NuXL:QQ_EXPLAINED_FRACTION", QQ_EXPLAINED_FRACTION[scan_index].quantileOfValue(ph.getMetaValue("NuXL:explained_peak_fraction"))); } - - - - } #endif - - /* // keep 10 bins with best 100 scores using priority queues vector best_score_per_bin(10, LargestElements(100)); @@ -5983,7 +6164,18 @@ static void scoreXLIons_( out2.substitute(".idXML", "_"); vector tmp_prots = protein_ids; IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); + // PSM result IdXMLFile().store(out2 + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); + + // protein result + if (!out_tsv.empty()) + { + out2 = out_tsv; + out2.substitute(".tsv", "_proteins"); + TextFile tsv_file; + annotateProteinModificationForTopHits_(tmp_prots, xl_pi, tsv_file); + tsv_file.store(out2 + String::number(xlFDR, 4) + "_XLs.tsv"); + } } } @@ -6003,11 +6195,11 @@ static void scoreXLIons_( process_params << "-in" << out_idxml.toQString() << "-out" << perc_out.toQString() << "-percolator_executable" << percolator_executable.toQString() - << "-train-best-positive" + << "-train_best_positive" << "-score_type" << "svm" << "-unitnorm" - << "-post-processing-tdc" -// << "-nested-xval-bins" << "3" + << "-post_processing_tdc" +// << "-nested_xval_bins" << "3" << "-weights" << weights_out.toQString() << "-out_pin" << pin.toQString(); @@ -6103,7 +6295,18 @@ static void scoreXLIons_( out2.substitute(".idXML", "_perc_"); vector tmp_prots = protein_ids; IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); + + // store PSM results IdXMLFile().store(out2 + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); + // store protein results + if (!out_tsv.empty()) + { + out2 = out_tsv; + out2.substitute(".tsv", "_perc_proteins"); + TextFile tsv_file; + annotateProteinModificationForTopHits_(tmp_prots, xl_pi, tsv_file); + tsv_file.store(out2 + String::number(xlFDR, 4) + "_XLs.tsv"); + } } } } @@ -6130,6 +6333,7 @@ static void scoreXLIons_( } csv_file.store(out_tsv); } + #ifdef _OPENMP // free locks From f34baa238ae2573b4e1d2510d253a2876124477f Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 25 Nov 2020 12:52:17 +0100 Subject: [PATCH 138/471] fix bug that led to some precusor adducts not being generated --- .../RNPXL/RNPxlModificationsGenerator.cpp | 32 +++++++++++-------- src/utils/OpenNuXL.cpp | 4 ++- 2 files changed, 21 insertions(+), 15 deletions(-) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp index ebc19f5113a..657fbf3f31c 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp @@ -82,7 +82,8 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse RNPxlModificationMassesResult result; - // read nucleotides and empirical formula of monophosphate + // read nucleotides and empirical formula of monophosphate. + // create map target->formula e.g., U->C10H14N5O7P map map_target_to_formula; for (auto const & s : target_nucleotides) { @@ -247,7 +248,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse { // Append precursor modifications (e.g., "-H2O") - // to generate modified nucleotides: e.g.: "U" -> "U", "U-H2O", ... + // to generate modified nucleotides: e.g.: "U" -> "U", "U-H2O", ... vector actual_combinations; for (map::const_iterator mit = map_target_to_formula.begin(); mit != map_target_to_formula.end(); ++mit) { @@ -256,12 +257,14 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse EmpiricalFormula target_nucleotide_formula = mit->second; + // get all precursor modifications for current nucleotide NucleotideModifications nt_mods = map_to_nucleotide_modifications[target_nucleotide]; - for (NucleotideModification const & nt_mod : nt_mods) // loop over list of nucleotide specific modifications + set formulas_of_modified_nucleotide; + for (const NucleotideModification & nt_mod : nt_mods) // loop over list of nucleotide specific modifications { EmpiricalFormula e(target_nucleotide_formula); - String s(target_nucleotide); + String nt(target_nucleotide); for (NucleotideModificationSubFormula const & sf : nt_mod) // loop over subformulae { // concatenate additive / subtractive substrings (e.g., "+H2O", "-H3PO") @@ -269,26 +272,27 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse String mod(sf.first.toString()); if (sf.second) { // subtractive - e = e - mod_ef; - s += "-" + mod; + nt += "-" + mod; // e.g., U-H2O + e = e - mod_ef; // sum formula of e.g. U-H2O } else { // additive - e = e + mod_ef; - s += "+" + mod;; + nt += "+" + mod; // e.g., U+H3PO4 + e = e + mod_ef; // sum formula } } - - if (find(actual_combinations.begin(), actual_combinations.end(), e) == actual_combinations.end()) + + String sum_formula_string = e.toString(); + if (find(formulas_of_modified_nucleotide.begin(), formulas_of_modified_nucleotide.end(), sum_formula_string) == formulas_of_modified_nucleotide.end()) { actual_combinations.push_back(e); - result.mod_combinations[e.toString()].insert(s); - OPENMS_LOG_INFO << "\t" << "modifications: " << s << "\t\t" << e.toString() << endl; + result.mod_combinations[sum_formula_string].insert(nt); // add sum formula -> nucleotide + OPENMS_LOG_INFO << "\t" << "modifications: " << nt << "\t\t" << sum_formula_string << endl; } else { - OPENMS_LOG_WARN << "WARNING:\tNucleotide combination: " << s << "\t\t" << e.toString() - << " occured several times. Did you specify it multiple times in the ini file?. Will consider only once." << endl; + OPENMS_LOG_WARN << "WARNING:\tNucleotide + formula combination: " << nt << "\t\t" << sum_formula_string + << " occured several times. Did you specify it multiple times in the ini file?. Will consider skip this entry." << endl; } } } diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index d2e1823ddc9..aa7f662e384 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -4366,7 +4366,9 @@ static void scoreXLIons_( for (const auto p2psm : position2psm_count) { while (p < p2psm.first) { annotated_sequence += seq[p]; ++p; } - annotated_sequence += "[" + String(p2psm.first + 1) + "," + String(p2psm.second) + "]"; + // p now points to the modified AA + annotated_sequence += String("[") + seq[p] + String(p2psm.first + 1) + "," + String(p2psm.second) + "]"; + ++p; } tsv_file.addLine(annotated_sequence); From 3b72901eba06d69c857ce9f6527a594d40c10fa1 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 26 Nov 2020 14:39:45 +0100 Subject: [PATCH 139/471] more extensive report --- src/utils/OpenNuXL.cpp | 71 +++++++++++++++++++++++++----------------- 1 file changed, 43 insertions(+), 28 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index aa7f662e384..5201997b3e7 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -4304,29 +4304,28 @@ static void scoreXLIons_( for (const PeptideIdentification& pep : peps) { auto& hits = pep.getHits(); - for (const PeptideHit& ph : hits) + if (hits.empty()) continue; + const PeptideHit& ph = hits[0]; // only consider top hit + const std::vector& ph_evidences = ph.getPeptideEvidences(); + const int best_localization = ph.getMetaValue("NuXL:best_localization_position"); + for (auto& ph_evidence : ph_evidences) { - const std::vector& ph_evidences = ph.getPeptideEvidences(); - const int best_localization = ph.getMetaValue("NuXL:best_localization_position"); - for (auto& ph_evidence : ph_evidences) - { - const String& acc = ph_evidence.getProteinAccession(); - const int peptide_start_in_protein = ph_evidence.getStart(); + const String& acc = ph_evidence.getProteinAccession(); + const int peptide_start_in_protein = ph_evidence.getStart(); - if (peptide_start_in_protein < 0 || best_localization < 0) continue; + if (peptide_start_in_protein < 0 || best_localization < 0) continue; - const int xl_pos_in_protein = peptide_start_in_protein + best_localization; + const int xl_pos_in_protein = peptide_start_in_protein + best_localization; - bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); - // retrieve protein the evidence points to - ProteinHit* protein = is_target ? acc2protein_targets[acc] : acc2protein_decoys[acc]; - if (xl_pos_in_protein < protein->getSequence().size()) - { - auto mods = protein->getModifications(); // TODO: add mutable reference access - mods.AALevelSummary[xl_pos_in_protein][*xl].count++; - protein->setModifications(mods); - } + // retrieve protein the evidence points to + ProteinHit* protein = is_target ? acc2protein_targets[acc] : acc2protein_decoys[acc]; + if (xl_pos_in_protein < protein->getSequence().size()) + { + auto mods = protein->getModifications(); // TODO: add mutable reference access + mods.AALevelSummary[xl_pos_in_protein][*xl].count++; + protein->setModifications(mods); } } } @@ -4335,13 +4334,17 @@ static void scoreXLIons_( map aa2psm_count_targets; // how many PSMs have that AA cross-linked map aa2protein_count_decoys; // how many proteins have that AA cross-linked map aa2psm_count_decoys; // how many PSMs have that AA cross-linked + + map aa2background_freq; // AA background distribution for normalization for (const ProteinIdentification& prot_id : prot_ids) { - const vector& proteins = prot_id.getHits(); for (const ProteinHit& protein : proteins) { const String& seq = protein.getSequence(); + + for (const char c : seq) { aa2background_freq[c] += 1.0; } + const String& acc = protein.getAccession(); bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); auto mods = protein.getModifications(); @@ -4363,14 +4366,22 @@ static void scoreXLIons_( // put string with AA, position, PSM count in sequence: e.g.: [Y123,2] String annotated_sequence; size_t p{0}; - for (const auto p2psm : position2psm_count) + + if (!position2psm_count.empty()) + { + for (const auto p2psm : position2psm_count) + { + while (p < p2psm.first) { annotated_sequence += seq[p]; ++p; } + // p now points to the modified AA + annotated_sequence += String("[") + seq[p] + String(p2psm.first + 1) + "," + String(p2psm.second) + "]"; + ++p; + } + tsv_file.addLine(annotated_sequence); + } + else { - while (p < p2psm.first) { annotated_sequence += seq[p]; ++p; } - // p now points to the modified AA - annotated_sequence += String("[") + seq[p] + String(p2psm.first + 1) + "," + String(p2psm.second) + "]"; - ++p; - } - tsv_file.addLine(annotated_sequence); + tsv_file.addLine(seq); + } set already_counted_at_protein_level; for (const auto& p2ms : mods.AALevelSummary) @@ -4415,6 +4426,10 @@ static void scoreXLIons_( } } } + + double sum{}; + for (const auto& m : aa2background_freq) { sum += m.second; } + for (auto& m : aa2background_freq) { m.second /= sum; } tsv_file.addLine("============================================================="); tsv_file.addLine("Protein summary for decoy proteins:"); @@ -4436,7 +4451,7 @@ static void scoreXLIons_( tsv_file.addLine("AA:proteins"); for (const auto& a2p : aa2protein_count_targets) { - tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second) + "\tfreq. normalized: " + String(a2p.second * aa2background_freq[a2p.first])); } tsv_file.addLine("============================================================="); @@ -4444,7 +4459,7 @@ static void scoreXLIons_( tsv_file.addLine("AA:PSMs"); for (const auto& a2p : aa2psm_count_targets) { - tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second) + "\tfreq. normalized: " + String(a2p.second * aa2background_freq[a2p.first])); } } From 68d359c1c9d1ab86cfc23903538ddbec56458868 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Fri, 27 Nov 2020 12:44:29 +0000 Subject: [PATCH 140/471] added probability --- .../include/OpenMS/METADATA/ProteinModificationSummary.h | 8 +++++--- src/openms/source/METADATA/ProteinModificationSummary.cpp | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h index d9959a68b64..3ef60ba120f 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h +++ b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h @@ -48,12 +48,14 @@ namespace OpenMS struct OPENMS_DLLAPI ProteinModificationSummary { /// basic modification statistic + /// values are constructed as unknown/NA and equal -1 struct OPENMS_DLLAPI Statistics { bool operator==(const Statistics& rhs) const; - size_t count = 0; /// total number of PSMs supporting the modification at this position - double frequency = 0.0; /// PSMs with modification / total number of PSMs - double FLR = 0.0; /// false localization rate + size_t count = -1; ///< total number of PSMs supporting the modification at this position + double frequency = -1.0; ///< PSMs with modification / total number of PSMs + double FLR = -1.0; ///< false localization rate + double probability = -1.0; ///< (localization) probability }; /// comparison operator diff --git a/src/openms/source/METADATA/ProteinModificationSummary.cpp b/src/openms/source/METADATA/ProteinModificationSummary.cpp index e75fef074a6..10e25f7dfee 100644 --- a/src/openms/source/METADATA/ProteinModificationSummary.cpp +++ b/src/openms/source/METADATA/ProteinModificationSummary.cpp @@ -43,5 +43,5 @@ bool ProteinModificationSummary::operator==(const ProteinModificationSummary& rh bool ProteinModificationSummary::Statistics::operator==(const Statistics& rhs) const { - return std::tie(count, frequency) == std::tie(rhs.count, rhs.frequency); + return std::tie(count, frequency, FLR, probability) == std::tie(rhs.count, rhs.frequency, rhs.FLR, rhs.probability); } From d904bb9681b83ddeac274a401dd2e75fd28e1596 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Sat, 28 Nov 2020 13:33:44 +0100 Subject: [PATCH 141/471] improved report --- .../RNPXL/RNPxlModificationsGenerator.h | 21 +++++++++++++++-- .../RNPXL/RNPxlModificationsGenerator.cpp | 8 +++---- .../ANALYSIS/RNPXL/RNPxlParameterParsing.cpp | 2 +- src/utils/OpenNuXL.cpp | 23 ++++++++++--------- 4 files changed, 36 insertions(+), 18 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h index 532517a1288..17daefaca25 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h @@ -49,8 +49,26 @@ namespace OpenMS struct OPENMS_DLLAPI RNPxlModificationMassesResult { + struct MyStringLengthCompare + { + bool operator () (const std::string & p_lhs, const std::string & p_rhs) + { + const size_t lhsLength = p_lhs.length() ; + const size_t rhsLength = p_rhs.length() ; + if(lhsLength == rhsLength) + { + return (p_lhs < p_rhs) ; // when two strings have the same + // length, defaults to the normal + // string comparison + } + return (lhsLength < rhsLength) ; // compares with the length + } + }; std::map mod_masses; ///< empirical formula -> mass - std::map > mod_combinations; ///< empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities) + + using NucleotideFormulas = std::set; + using MapSumFormulaToNucleotideFormulas = std::map; + MapSumFormulaToNucleotideFormulas mod_combinations; ///< empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities) }; class OPENMS_DLLAPI RNPxlModificationsGenerator @@ -70,4 +88,3 @@ namespace OpenMS }; } - diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp index 657fbf3f31c..a6db0210949 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp @@ -314,7 +314,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse { new_combinations.push_back(target_nucleotide_formula + ac - EmpiricalFormula("H2O")); // -H2O because of condensation reaction all_combinations.push_back(target_nucleotide_formula + ac - EmpiricalFormula("H2O")); // " " - const set& ambiguities = result.mod_combinations[ac.toString()]; + const auto& ambiguities = result.mod_combinations[ac.toString()]; for (auto const & s : ambiguities) { result.mod_combinations[all_combinations.back().toString()].insert(target_nucleotide + s); @@ -346,7 +346,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse for (Map::ConstIterator mit = result.mod_masses.begin(); mit != result.mod_masses.end(); ++mit) { // remove additive or subtractive modifications from string as these are not used in string comparison - const set& ambiguities = result.mod_combinations[mit->first]; + const RNPxlModificationMassesResult::NucleotideFormulas& ambiguities = result.mod_combinations[mit->first]; for (String const & s : ambiguities) { String nucleotide_style_formula(s); @@ -434,7 +434,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse } // standard associative-container erase idiom - for (map >::iterator mcit = result.mod_combinations.begin(); mcit != result.mod_combinations.end(); ) + for (auto mcit = result.mod_combinations.begin(); mcit != result.mod_combinations.end(); ) { if (mcit->second.empty()) { @@ -468,7 +468,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse OPENMS_LOG_INFO << "Precursor adduct " << index++ << "\t:\t" << m.first << " " << m.second << " ( "; - const set& ambiguities = result.mod_combinations[m.first]; + const RNPxlModificationMassesResult::NucleotideFormulas& ambiguities = result.mod_combinations[m.first]; set printed; // for all ambiguities (same empirical formula) diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp index bcfba3b707e..dc942ef9493 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp @@ -65,7 +65,7 @@ RNPxlParameterParsing::getAllFeasibleFragmentAdducts( // get all precursor nucleotide formulas matching current empirical formula/mass const String& ef = pa.first; const double pc_mass = pa.second; - const set& ambiguities = precursor_adducts.mod_combinations.at(ef); + const auto& ambiguities = precursor_adducts.mod_combinations.at(ef); if (ambiguities.size() >= 2) { diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 5201997b3e7..632ecc6d830 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -2692,7 +2692,7 @@ static void scoreXLIons_( const double fixed_and_variable_modified_peptide_weight = fixed_and_variable_modified_peptide.getMonoWeight(); // determine NA on precursor from index in map - std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); + auto mod_combinations_it = mm.mod_combinations.cbegin(); std::advance(mod_combinations_it, a.rna_mod_index); const String precursor_rna_adduct = *mod_combinations_it->second.begin(); const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); @@ -3428,7 +3428,7 @@ static void scoreXLIons_( ph.setMetaValue(String("variable_modifications"), n_var_mods); // determine NA modification from index in map - std::map >::const_iterator mod_combinations_it = mm.mod_combinations.begin(); + auto mod_combinations_it = mm.mod_combinations.cbegin(); std::advance(mod_combinations_it, ah.rna_mod_index); ph.setMetaValue(String("NuXL:mass_error_p"), ah.mass_error_p); ph.setMetaValue(String("NuXL:total_loss_score"), ah.total_loss_score); @@ -4280,11 +4280,6 @@ static void scoreXLIons_( ProteinIdentification& prot_id = prot_ids[0]; vector& proteins = prot_id.getHits(); - // create a user defined modification - ResidueModification* xl = new ResidueModification(); - xl->setFullId("x"); // something not used in ResidueDB - xl->setOrigin('X'); // any AA - // create lookup accession -> protein map acc2protein_targets; map acc2protein_decoys; @@ -4308,6 +4303,12 @@ static void scoreXLIons_( const PeptideHit& ph = hits[0]; // only consider top hit const std::vector& ph_evidences = ph.getPeptideEvidences(); const int best_localization = ph.getMetaValue("NuXL:best_localization_position"); + + // create a user defined modification + ResidueModification* xl = new ResidueModification(); + xl->setFullId(ph.getMetaValue("NuXL:NA")); // something not used in ResidueDB + xl->setOrigin('X'); // any AA + for (auto& ph_evidence : ph_evidences) { const String& acc = ph_evidence.getProteinAccession(); @@ -4346,18 +4347,18 @@ static void scoreXLIons_( for (const char c : seq) { aa2background_freq[c] += 1.0; } const String& acc = protein.getAccession(); + tsv_file.addLine(acc); + bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); auto mods = protein.getModifications(); - tsv_file.addLine(acc); - // count how many PSMs support XL-ed position in a protein map position2psm_count; for (const auto& p2ms : mods.AALevelSummary) { size_t position = p2ms.first; for (const auto& m2s : p2ms.second) - { + { const auto stat = m2s.second; position2psm_count[position] += stat.count; } @@ -4421,7 +4422,7 @@ static void scoreXLIons_( { aa2psm_count_decoys[AA_at_position] += count; } - tsv_file.addLine(m2s.first.getFullId() + ":" + AA_at_position + String(position) + "(" + String(count) + ")"); + tsv_file.addLine(m2s.first.getFullId() + ":" + AA_at_position + String(position + 1) + "(" + String(count) + ")"); } } } From cdc63d15aae6f84b8f7f535f31f19dbd33123ad5 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Mon, 30 Nov 2020 21:38:05 +0100 Subject: [PATCH 142/471] [DOC] some parameter documentation --- .../RNPXL/RNPxlModificationsGenerator.h | 26 ++++++++-- .../RNPXL/RNPxlModificationsGenerator.cpp | 52 +++++++++---------- .../ANALYSIS/RNPXL/RNPxlParameterParsing.cpp | 2 +- src/utils/OpenNuXL.cpp | 42 +++++++-------- 4 files changed, 71 insertions(+), 51 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h index 17daefaca25..fb87d2c7655 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h @@ -47,6 +47,15 @@ namespace OpenMS { class AASequence; + /* + formula2mass holds the map from empirical formula to mass + + mod_combinations holds the map from empirical formula to (potentially ambigious) nucleotide formulae + e.g.,: + C10H14N5O7P -> {A} + C10H14N5O8P -> {G} + C18H22N4O16P2 -> { CU-H3N1, UU-H2O1 } + */ struct OPENMS_DLLAPI RNPxlModificationMassesResult { struct MyStringLengthCompare @@ -64,7 +73,7 @@ namespace OpenMS return (lhsLength < rhsLength) ; // compares with the length } }; - std::map mod_masses; ///< empirical formula -> mass + std::map formula2mass; ///< empirical formula -> mass using NucleotideFormulas = std::set; using MapSumFormulaToNucleotideFormulas = std::map; @@ -74,16 +83,27 @@ namespace OpenMS class OPENMS_DLLAPI RNPxlModificationsGenerator { public: + /* @brief generate all combinations of precursor adducts + @param target_nucleotides the list of nucleotides: e.g., "U", "C", "G", "A" or "U", "T", "G", "A" + @param can_xl the set of cross-linkable nucleotides + @param mappings + @param modifications additional losses associated with the precursor adduct: e.g., "-H2O" + @param sequence_restriction only precursor adducts that are substrings of this NA sequence are generated + @param cysteine_adduct special DTT adduct + @param max_length maximum oligo length + */ static RNPxlModificationMassesResult initModificationMassesNA(StringList target_nucleotides, StringList nt_groups, std::set can_xl, StringList mappings, StringList modifications, - String sequence_restriction, - bool cysteine_adduct, + String sequence_restriction = "", + bool cysteine_adduct = false, Int max_length = 4); private: + /// return true if qery is not in sequence static bool notInSeq(String res_seq, String query); + static void generateTargetSequences(const String& res_seq, Size param_pos, const std::map >& map_source2target, StringList& target_sequences); }; } diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp index a6db0210949..d1ef168ef84 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlModificationsGenerator.cpp @@ -101,7 +101,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse map_source_to_targets[fields[0][0]].push_back(fields[1][0]); } - // extract source nucleotides based on mapping + // extract source nucleotides based on mapping (if provided) vector source_nucleotides; // nucleotides as expected in the restriction sequence for (auto const & s : mappings) { @@ -141,8 +141,11 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse } } - // erase trivial cases from mapping so only the combinatorial cases: 1 source -> n targets remain - for (map >::iterator sit = map_source_to_targets.begin(); sit != map_source_to_targets.end(); ) + // erase trivial cases: + // 1. identity: only A->A provided + // 2. rename: only A->X provided + // but keep cominatorial cases: e.g., both A->X and A->A provided. + for (auto sit = map_source_to_targets.begin(); sit != map_source_to_targets.end(); ) { char source = sit->first; char first_target = sit->second[0]; @@ -162,11 +165,10 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse } } - // std::cout << "source sequence: " << sequence_restriction << endl; - if (!map_source_to_targets.empty() && sequence_restriction.empty()) { - OPENMS_LOG_WARN << "WARNING: no restriction on sequence but multiple target nucleotides specified. Will generate huge amount of sequences" << endl; + OPENMS_LOG_WARN << "WARNING: no restriction on sequence but multiple target nucleotides specified." + << "May generate huge amount of sequences considered as adduct." << endl; } using NucleotideModificationSubFormula = pair; // e.g., "H2O", true @@ -229,7 +231,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse StringList target_sequences; generateTargetSequences(sequence_restriction, 0, map_source_to_targets, target_sequences); - OPENMS_LOG_INFO << "target sequence(s):" << target_sequences.size() << endl; + OPENMS_LOG_INFO << "sequence(s):" << target_sequences.size() << endl; if (!original_sequence_restriction.empty()) { @@ -250,10 +252,10 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse // Append precursor modifications (e.g., "-H2O") // to generate modified nucleotides: e.g.: "U" -> "U", "U-H2O", ... vector actual_combinations; - for (map::const_iterator mit = map_target_to_formula.begin(); mit != map_target_to_formula.end(); ++mit) + for (auto mit = map_target_to_formula.cbegin(); mit != map_target_to_formula.cend(); ++mit) { String target_nucleotide = mit->first; - OPENMS_LOG_INFO << "target nucleotide: " << target_nucleotide << endl; + OPENMS_LOG_INFO << "nucleotide: " << target_nucleotide << endl; EmpiricalFormula target_nucleotide_formula = mit->second; @@ -263,7 +265,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse set formulas_of_modified_nucleotide; for (const NucleotideModification & nt_mod : nt_mods) // loop over list of nucleotide specific modifications { - EmpiricalFormula e(target_nucleotide_formula); + EmpiricalFormula sum_formula(target_nucleotide_formula); String nt(target_nucleotide); for (NucleotideModificationSubFormula const & sf : nt_mod) // loop over subformulae { @@ -273,25 +275,24 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse if (sf.second) { // subtractive nt += "-" + mod; // e.g., U-H2O - e = e - mod_ef; // sum formula of e.g. U-H2O + sum_formula = sum_formula - mod_ef; // sum formula of e.g. U-H2O } else { // additive nt += "+" + mod; // e.g., U+H3PO4 - e = e + mod_ef; // sum formula + sum_formula = sum_formula + mod_ef; // sum formula } } - String sum_formula_string = e.toString(); - if (find(formulas_of_modified_nucleotide.begin(), formulas_of_modified_nucleotide.end(), sum_formula_string) == formulas_of_modified_nucleotide.end()) + if (formulas_of_modified_nucleotide.find(sum_formula.toString()) == formulas_of_modified_nucleotide.end()) { - actual_combinations.push_back(e); - result.mod_combinations[sum_formula_string].insert(nt); // add sum formula -> nucleotide - OPENMS_LOG_INFO << "\t" << "modifications: " << nt << "\t\t" << sum_formula_string << endl; + actual_combinations.push_back(sum_formula); + result.mod_combinations[sum_formula.toString()].insert(nt); // add sum formula -> nucleotide + OPENMS_LOG_INFO << "\t" << "modifications: " << nt << "\t\t" << sum_formula.toString() << endl; } else { - OPENMS_LOG_WARN << "WARNING:\tNucleotide + formula combination: " << nt << "\t\t" << sum_formula_string + OPENMS_LOG_WARN << "WARNING:\tNucleotide + formula combination: " << nt << "\t\t" << sum_formula.toString() << " occured several times. Did you specify it multiple times in the ini file?. Will consider skip this entry." << endl; } } @@ -327,7 +328,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse for (Size i = 0; i != all_combinations.size(); ++i) { - result.mod_masses[all_combinations[i].toString()] = all_combinations[i].getMonoWeight(); + result.formula2mass[all_combinations[i].toString()] = all_combinations[i].getMonoWeight(); } } @@ -343,7 +344,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse std::vector > unique_nucleotide_and_mod_composition; std::vector > violates_restriction; // elemental composition, nucleotide style formula - for (Map::ConstIterator mit = result.mod_masses.begin(); mit != result.mod_masses.end(); ++mit) + for (Map::ConstIterator mit = result.formula2mass.begin(); mit != result.formula2mass.end(); ++mit) { // remove additive or subtractive modifications from string as these are not used in string comparison const RNPxlModificationMassesResult::NucleotideFormulas& ambiguities = result.mod_combinations[mit->first]; @@ -374,7 +375,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse } // check if nucleotide sequence too long - if (nucleotide_style_formula.size() > max_length) + if ((int)nucleotide_style_formula.size() > max_length) { violates_restriction.push_back(make_pair(mit->first, s)); continue; @@ -438,7 +439,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse { if (mcit->second.empty()) { - result.mod_masses.erase(mcit->first); // remove from mod masses + result.formula2mass.erase(mcit->first); // remove from mod masses result.mod_combinations.erase(mcit++); // don't change precedence ! } else @@ -450,7 +451,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse // Optional: add cystein (DTT) adduct if (cysteine_adduct) { - result.mod_masses[cysteine_adduct_formula.toString()] = cysteine_adduct_formula.getMonoWeight(); + result.formula2mass[cysteine_adduct_formula.toString()] = cysteine_adduct_formula.getMonoWeight(); result.mod_combinations[cysteine_adduct_formula.toString()].insert(cysteine_adduct_string); } @@ -458,7 +459,7 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse // nucleotide formulas which only differ in nucleotide ordering are only printed once // e.g. 5 C19H24N7O12P1 573.122 ( AU-H1O3P1 ) double index = 1; - for (auto const & m : result.mod_masses) + for (auto const & m : result.formula2mass) { if (cysteine_adduct && m.first == cysteine_adduct_formula.toString()) { @@ -472,9 +473,8 @@ RNPxlModificationMassesResult RNPxlModificationsGenerator::initModificationMasse set printed; // for all ambiguities (same empirical formula) - for (set::const_iterator sit = ambiguities.begin(); sit != ambiguities.end(); ++sit) + for (String nucleotide_style_formula : ambiguities) { - String nucleotide_style_formula = *sit; Size p1 = nucleotide_style_formula.find('-'); Size p2 = nucleotide_style_formula.find('+'); Size p = min(p1, p2); diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp index dc942ef9493..b89f4ca6a49 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp @@ -60,7 +60,7 @@ RNPxlParameterParsing::getAllFeasibleFragmentAdducts( map> mass_frags2pc_xlnuc; // for all distinct precursor adduct formulas/masses - for (auto const & pa : precursor_adducts.mod_masses) + for (auto const & pa : precursor_adducts.formula2mass) { // get all precursor nucleotide formulas matching current empirical formula/mass const String& ef = pa.first; diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 632ecc6d830..b4c86630623 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -234,7 +234,7 @@ class AnnotatedHit */ StringView sequence; SignedSize peptide_mod_index = 0; // enumeration index of the non-NA peptide modification - Size rna_mod_index = 0; // index of the NA modification + Size NA_mod_index = 0; // index of the NA modification int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment @@ -2477,8 +2477,8 @@ static void scoreXLIons_( { // determine NA on precursor from index in map auto mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, annotated_hits[scan_index][i].rna_mod_index); - const String precursor_rna_adduct = *mod_combinations_it->second.begin(); + std::advance(mod_combinations_it, annotated_hits[scan_index][i].NA_mod_index); // advance to sum formula at index NA_mod_index + const String precursor_rna_adduct = *mod_combinations_it->second.begin(); // get first nucleotide formula e.g. UU-H2O TODO:is this correct? only handle the first????????????????????????????????????????????????????????????????????? const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; if (precursor_rna_adduct == "none") @@ -2518,7 +2518,7 @@ static void scoreXLIons_( // determine NA on precursor from index in map auto mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, ah.rna_mod_index); + std::advance(mod_combinations_it, ah.NA_mod_index); const String precursor_rna_adduct = *mod_combinations_it->second.begin(); const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; @@ -2693,8 +2693,8 @@ static void scoreXLIons_( // determine NA on precursor from index in map auto mod_combinations_it = mm.mod_combinations.cbegin(); - std::advance(mod_combinations_it, a.rna_mod_index); - const String precursor_rna_adduct = *mod_combinations_it->second.begin(); + std::advance(mod_combinations_it, a.NA_mod_index); + const String precursor_rna_adduct = *mod_combinations_it->second.begin(); // TODO: check if it is enough to consider only first precursor adduct ???????????????????????????????????????????????????????? const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); // we don't localize on non-cross-links @@ -3429,7 +3429,7 @@ static void scoreXLIons_( // determine NA modification from index in map auto mod_combinations_it = mm.mod_combinations.cbegin(); - std::advance(mod_combinations_it, ah.rna_mod_index); + std::advance(mod_combinations_it, ah.NA_mod_index); ph.setMetaValue(String("NuXL:mass_error_p"), ah.mass_error_p); ph.setMetaValue(String("NuXL:total_loss_score"), ah.total_loss_score); ph.setMetaValue(String("NuXL:immonium_score"), ah.immonium_score); @@ -3457,7 +3457,7 @@ static void scoreXLIons_( ph.setMetaValue(String("NuXL:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses - String NA = *mod_combinations_it->second.begin(); + String NA = *mod_combinations_it->second.begin(); // TODO: consider only first (potentially ambigious one) ?????????????????????????????????????? ph.setMetaValue(String("NuXL:NA"), NA); // return first nucleotide formula matching the index of the empirical formula double na_mass_z0 = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); // NA uncharged mass via empirical formula @@ -3841,7 +3841,7 @@ static void scoreXLIons_( ah.total_MIC = tlss_total_MIC; - ah.rna_mod_index = rna_mod_idx; + ah.NA_mod_index = rna_mod_idx; ah.isotope_error = isotope_error; auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); @@ -4851,7 +4851,7 @@ static void scoreXLIons_( if (!getFlag_("RNPxl:only_xl")) { - mm.mod_masses[""] = 0; // insert "null" modification otherwise peptides without NA will not be searched + mm.formula2mass[""] = 0; // insert "null" modification otherwise peptides without NA will not be searched mm.mod_combinations[""].insert("none"); } @@ -5170,11 +5170,11 @@ static void scoreXLIons_( PeakSpectrum marker_ions_sub_score_spectrum; // iterate over all NA sequences, calculate peptide mass and generate complete loss spectrum only once as this can potentially be reused - Size rna_mod_index = 0; + Size NA_mod_index = 0; - for (std::map::const_iterator rna_mod_it = mm.mod_masses.begin(); - rna_mod_it != mm.mod_masses.end(); - ++rna_mod_it, ++rna_mod_index) + for (std::map::const_iterator rna_mod_it = mm.formula2mass.begin(); + rna_mod_it != mm.formula2mass.end(); + ++rna_mod_it, ++NA_mod_index) { const double precursor_rna_mass = rna_mod_it->second; const double current_peptide_mass = current_peptide_mass_without_NA + precursor_rna_mass; // add NA mass @@ -5211,8 +5211,8 @@ static void scoreXLIons_( { // retrieve NA adduct name auto mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, rna_mod_index); - const String& precursor_rna_adduct = *mod_combinations_it->second.begin(); + std::advance(mod_combinations_it, NA_mod_index); + const String& precursor_rna_adduct = *mod_combinations_it->second.begin(); // TODO: check if sufficient to consider only first NA adduct here ????????????????????????????????????????????????????????????????????? if (precursor_rna_adduct == "none") { @@ -5295,7 +5295,7 @@ static void scoreXLIons_( ah.precursor_score = pc_MIC; ah.total_MIC = tlss_total_MIC; - ah.rna_mod_index = rna_mod_index; + ah.NA_mod_index = NA_mod_index; ah.isotope_error = isotope_error; auto range = make_pair(intensity_linear.begin(), intensity_linear.end()); @@ -5542,7 +5542,7 @@ static void scoreXLIons_( ah.marker_ions_score = marker_ions_sub_score; ah.partial_loss_score = partial_loss_sub_score; - ah.rna_mod_index = rna_mod_index; + ah.NA_mod_index = NA_mod_index; ah.isotope_error = isotope_error; auto range = make_pair(intensity_linear.begin(), intensity_linear.end()); @@ -5609,8 +5609,8 @@ static void scoreXLIons_( { const Size & scan_index = l->second.first; auto mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, rna_mod_index); - const String& precursor_rna_adduct = *mod_combinations_it->second.begin(); + std::advance(mod_combinations_it, NA_mod_index); + const String& precursor_rna_adduct = *mod_combinations_it->second.begin(); // For fast scoring it should be sufficient to only consider any of the adducts for this mass and formula (e.g., C-H3N vs U-H2O) MSSpectrum& exp_spectrum = spectra[scan_index]; if (precursor_rna_adduct != "none" && skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) continue; @@ -5635,7 +5635,7 @@ static void scoreXLIons_( spectra[scan_index], *cit, // string view on unmodified sequence mod_pep_idx, // index of peptide mod - rna_mod_index, // index of RNA mod + NA_mod_index, // index of NA mod current_peptide_mass, current_peptide_mass_without_NA, exp_pc_mass, From 7fc4a4c72caadf0100e1bfb760d18f97b165c0ed Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 1 Dec 2020 10:00:56 +0100 Subject: [PATCH 143/471] dont't report decoy proteins by default --- src/utils/OpenNuXL.cpp | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index b4c86630623..61f1dadc0a8 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -4273,7 +4273,7 @@ static void scoreXLIons_( return EXECUTION_OK; } - void annotateProteinModificationForTopHits_(vector& prot_ids, const vector& peps, TextFile& tsv_file) + void annotateProteinModificationForTopHits_(vector& prot_ids, const vector& peps, TextFile& tsv_file, bool output_decoys = false) { assert(prots.size() == 1); // support for one run only @@ -4432,21 +4432,25 @@ static void scoreXLIons_( for (const auto& m : aa2background_freq) { sum += m.second; } for (auto& m : aa2background_freq) { m.second /= sum; } - tsv_file.addLine("============================================================="); - tsv_file.addLine("Protein summary for decoy proteins:"); - tsv_file.addLine("AA:proteins"); - for (const auto& a2p : aa2protein_count_decoys) + if (output_decoys) { - tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); - } + tsv_file.addLine("============================================================="); + tsv_file.addLine("Protein summary for decoy proteins:"); + tsv_file.addLine("AA:proteins"); + for (const auto& a2p : aa2protein_count_decoys) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + } - tsv_file.addLine("============================================================="); - tsv_file.addLine("PSM summary for decoy PSMs:"); - tsv_file.addLine("AA:PSMs"); - for (const auto& a2p : aa2psm_count_decoys) - { - tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + tsv_file.addLine("============================================================="); + tsv_file.addLine("PSM summary for decoy PSMs:"); + tsv_file.addLine("AA:PSMs"); + for (const auto& a2p : aa2psm_count_decoys) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + } } + tsv_file.addLine("============================================================="); tsv_file.addLine("Protein summary for target proteins:"); tsv_file.addLine("AA:proteins"); From 673cc36dae45bcf97eef3b3492d855bc8922ff4f Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 2 Dec 2020 11:15:13 +0100 Subject: [PATCH 144/471] annotate XL regions --- src/utils/OpenNuXL.cpp | 91 +++++++++++++++++++++++++++++++++++------- 1 file changed, 76 insertions(+), 15 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 61f1dadc0a8..8b2cd4a9818 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -4273,16 +4273,10 @@ static void scoreXLIons_( return EXECUTION_OK; } - void annotateProteinModificationForTopHits_(vector& prot_ids, const vector& peps, TextFile& tsv_file, bool output_decoys = false) - { - assert(prots.size() == 1); // support for one run only - ProteinIdentification& prot_id = prot_ids[0]; + void mapAccessionToTDProteins(ProteinIdentification& prot_id, map& acc2protein_targets, map& acc2protein_decoys) + { vector& proteins = prot_id.getHits(); - - // create lookup accession -> protein - map acc2protein_targets; - map acc2protein_decoys; for (ProteinHit& protein : proteins) { if (protein.getMetaValue("target_decoy").toString().hasPrefix("target")) @@ -4294,6 +4288,34 @@ static void scoreXLIons_( acc2protein_decoys[protein.getAccession()] = &protein; } } + } + + void annotateProteinModificationForTopHits_(vector& prot_ids, const vector& peps, TextFile& tsv_file, bool report_decoys = false) + { + assert(prots.size() == 1); // support for one run only + + // protein identification run + ProteinIdentification& prot_id = prot_ids[0]; + + // create lookup accession -> protein + map acc2protein_targets; + map acc2protein_decoys; + mapAccessionToTDProteins(prot_id, acc2protein_targets, acc2protein_decoys); + + struct ModifiedRegion + { + ResidueModification* xl; + int first; + int last; + bool operator<(const ModifiedRegion& rhs) const + { + return std::tie(first, last, *xl) < std::tie(rhs.first, rhs.last, *rhs.xl); + } + }; + + // protein -> regions with XLs without AA level localization and in how many PSMs it was detected + map> modified_region_xls_targets; + map> modified_region_xls_decoys; // store modification statistic for every protein for (const PeptideIdentification& pep : peps) @@ -4314,12 +4336,28 @@ static void scoreXLIons_( const String& acc = ph_evidence.getProteinAccession(); const int peptide_start_in_protein = ph_evidence.getStart(); - if (peptide_start_in_protein < 0 || best_localization < 0) continue; - + if (peptide_start_in_protein < 0) continue; + const int xl_pos_in_protein = peptide_start_in_protein + best_localization; bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + if (best_localization < 0) + { + ModifiedRegion mr; + mr.xl = xl; + mr.first = ph_evidence.getStart(); + mr.last = ph_evidence.getEnd(); + if (is_target) + { + modified_region_xls_targets[acc][mr]++; + } + else + { + modified_region_xls_decoys[acc][mr]++; + } + } + // retrieve protein the evidence points to ProteinHit* protein = is_target ? acc2protein_targets[acc] : acc2protein_decoys[acc]; if (xl_pos_in_protein < protein->getSequence().size()) @@ -4340,16 +4378,19 @@ static void scoreXLIons_( for (const ProteinIdentification& prot_id : prot_ids) { - for (const ProteinHit& protein : proteins) + const vector& phs = prot_id.getHits(); + for (const ProteinHit& protein : phs) { + const String& acc = protein.getAccession(); + bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + + if (!is_target && !report_decoys) continue; // skip decoys if option is set + const String& seq = protein.getSequence(); for (const char c : seq) { aa2background_freq[c] += 1.0; } - - const String& acc = protein.getAccession(); tsv_file.addLine(acc); - bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); auto mods = protein.getModifications(); // count how many PSMs support XL-ed position in a protein @@ -4377,6 +4418,8 @@ static void scoreXLIons_( annotated_sequence += String("[") + seq[p] + String(p2psm.first + 1) + "," + String(p2psm.second) + "]"; ++p; } + while (p < seq.size()) { annotated_sequence += seq[p]; ++p; } // output AAs after last modification + tsv_file.addLine(annotated_sequence); } else @@ -4384,6 +4427,7 @@ static void scoreXLIons_( tsv_file.addLine(seq); } + // output modification AA and count for this protein set already_counted_at_protein_level; for (const auto& p2ms : mods.AALevelSummary) { @@ -4425,6 +4469,17 @@ static void scoreXLIons_( tsv_file.addLine(m2s.first.getFullId() + ":" + AA_at_position + String(position + 1) + "(" + String(count) + ")"); } } + + // output list of modified regions (without AA level localization) + for (const auto& p2xlregions : modified_region_xls_targets) + { + for (const auto& region : p2xlregions.second) + { + const ModifiedRegion& r = region.first; + const size_t count = region.second; + tsv_file.addLine(r.xl->getFullId() + ":" + String(r.first + 1) + "-" + String(r.last + 1) + "(" + String(count) + ")"); + } + } } } @@ -4432,7 +4487,7 @@ static void scoreXLIons_( for (const auto& m : aa2background_freq) { sum += m.second; } for (auto& m : aa2background_freq) { m.second /= sum; } - if (output_decoys) + if (report_decoys) { tsv_file.addLine("============================================================="); tsv_file.addLine("Protein summary for decoy proteins:"); @@ -6158,6 +6213,11 @@ static void scoreXLIons_( fdr.apply(xl_pi); fdr.apply(pep_pi); + if (debug_level_ > 1) + { + + } + IDFilter::removeDecoyHits(xl_pi); IDFilter::removeDecoyHits(pep_pi); @@ -6165,6 +6225,7 @@ static void scoreXLIons_( { IDFilter::filterHitsByScore(pep_pi, peptide_FDR); } + { String out2(out_idxml); out2.substitute(".idXML", "_"); From 30e75d9e2bd659822dfd202bc54c2de15a179f2d Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 3 Dec 2020 15:55:33 +0000 Subject: [PATCH 145/471] changed default initialization back --- .../METADATA/ProteinModificationSummary.h | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h index 3ef60ba120f..4cca16dc72d 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h +++ b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h @@ -29,7 +29,7 @@ // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ -// $Authors: $ +// $Authors: Timo Sachsenberg $ // -------------------------------------------------------------------------- #pragma once @@ -40,22 +40,24 @@ namespace OpenMS { /** - * @brief Maps a protein position to all observed modifications and associated statistics - * - * For example, to store that position 10 maps to Oxidation (M) which was observed in 123 PSMs. + * @brief Map a protein position to all observed modifications and associated statistics * + * For example, allows storing that position 10 in the protein carries Oxidation (M) + * and was observed in 123 PSMs. + * Note: Implementation uses a std::map, thus accessing a location not present in the map + * with operator[] will value construct an empty map at that location. Like with std::maps + * check first if the key exists. */ struct OPENMS_DLLAPI ProteinModificationSummary { /// basic modification statistic - /// values are constructed as unknown/NA and equal -1 struct OPENMS_DLLAPI Statistics { bool operator==(const Statistics& rhs) const; - size_t count = -1; ///< total number of PSMs supporting the modification at this position - double frequency = -1.0; ///< PSMs with modification / total number of PSMs - double FLR = -1.0; ///< false localization rate - double probability = -1.0; ///< (localization) probability + size_t count = 0; ///< total number of PSMs supporting the modification at this position + double frequency = 0.0; ///< PSMs with modification / total number of PSMs + double FLR = 0.0; ///< false localization rate + double probability = 0.0; ///< (localization) probability }; /// comparison operator @@ -67,5 +69,4 @@ namespace OpenMS /// position -> modification -> statistic (counts, etc.) AALevelModificationSummary AALevelSummary; }; - } From b6c8cc9174a5ecab894012d85c7c06c35c7cc598 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 4 Dec 2020 15:19:46 +0100 Subject: [PATCH 146/471] attempt to compensate length bias --- .../METADATA/ProteinModificationSummary.h | 14 ++++--- .../source/CHEMISTRY/DecoyGenerator.cpp | 12 +++++- .../METADATA/ProteinModificationSummary.cpp | 6 +++ src/utils/OpenNuXL.cpp | 41 +++++++++++++------ 4 files changed, 54 insertions(+), 19 deletions(-) diff --git a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h index b87dfbeaf47..39a39abbba1 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h +++ b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h @@ -29,14 +29,13 @@ // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ -// $Authors: $ +// $Authors: Timo Sachsenberg$ // -------------------------------------------------------------------------- #pragma once #include -#include #include namespace OpenMS @@ -50,10 +49,13 @@ namespace OpenMS struct OPENMS_DLLAPI ProteinModificationSummary { /// basic modification statistic - struct OPENMS_DLLAPI Statistics : public MetaInfoInterface + struct OPENMS_DLLAPI Statistics { - size_t count = 0; - double frequency = 0.0; + bool operator==(const Statistics& rhs) const; + size_t count = -1; ///< total number of PSMs supporting the modification at this position + double frequency = -1.0; ///< PSMs with modification / total number of PSMs + double FLR = -1.0; ///< false localization rate + double probability = -1.0; ///< (localization) probability }; /// comparison operator @@ -65,5 +67,5 @@ namespace OpenMS /// position -> modification -> statistic (counts, etc.) AALevelModificationSummary AALevelSummary; }; - } + diff --git a/src/openms/source/CHEMISTRY/DecoyGenerator.cpp b/src/openms/source/CHEMISTRY/DecoyGenerator.cpp index 4832e1d55ef..7786a83144b 100644 --- a/src/openms/source/CHEMISTRY/DecoyGenerator.cpp +++ b/src/openms/source/CHEMISTRY/DecoyGenerator.cpp @@ -151,7 +151,17 @@ double DecoyGenerator::SequenceIdentity_(const String& decoy, const String& targ if (target[i] == decoy[i]) { ++match; } } double identity = (double) match / target.size(); - return identity; + + // also compare against reverse + match = 0; + for (int i = (int)target.size() - 1; i >= 0; --i) + { + int j = (int)target.size() - 1 - i; + if (target[j] == decoy[i]) { ++match; } + } + double rev_identity = (double) match / target.size(); + + return std::max(identity, rev_identity); } diff --git a/src/openms/source/METADATA/ProteinModificationSummary.cpp b/src/openms/source/METADATA/ProteinModificationSummary.cpp index deea4790f61..92761e95476 100644 --- a/src/openms/source/METADATA/ProteinModificationSummary.cpp +++ b/src/openms/source/METADATA/ProteinModificationSummary.cpp @@ -40,3 +40,9 @@ bool ProteinModificationSummary::operator==(const ProteinModificationSummary& rh { return AALevelSummary == rhs.AALevelSummary; } + +bool ProteinModificationSummary::Statistics::operator==(const Statistics& rhs) const +{ + return std::tie(count, frequency, FLR, probability) == std::tie(rhs.count, rhs.frequency, rhs.FLR, rhs.probability); +} + diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 8b2cd4a9818..384bfd75cb6 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -51,6 +51,7 @@ #include #include #include +#include #include #include @@ -1593,7 +1594,7 @@ score += ah.mass_error_p * 1.15386068 + 11.45 * ah.ladder_score + 28.09 * (ah.tag_shifted >= 1); */ - return 1.0 * ah.total_loss_score + const double ret = 1.0 * ah.total_loss_score + 0.5 * ah.partial_loss_score + 1.0 * ah.mass_error_p - 0.1 * ah.err @@ -1604,6 +1605,7 @@ score += ah.mass_error_p * 1.15386068 // + 1.0 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) + 0.1 * ah.ladder_score + 1.0 * (ah.tag_shifted >= 1); + return ret; /* @@ -3819,6 +3821,8 @@ static void scoreXLIons_( const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); + total_loss_score = total_loss_score - 0.22 * (double)sequence.size(); + // early-out if super bad score if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { return; } @@ -3832,6 +3836,7 @@ static void scoreXLIons_( ah.sequence = sequence; // copy StringView ah.peptide_mod_index = mod_pep_idx; ah.total_loss_score = total_loss_score; + ah.MIC = tlss_MIC; ah.err = tlss_err; ah.Morph = tlss_Morph; @@ -4428,6 +4433,7 @@ static void scoreXLIons_( } // output modification AA and count for this protein + tsv_file.addLine("Cross-link localizations:"); set already_counted_at_protein_level; for (const auto& p2ms : mods.AALevelSummary) { @@ -4471,6 +4477,7 @@ static void scoreXLIons_( } // output list of modified regions (without AA level localization) + tsv_file.addLine("Cross-linked peptides without localization at single AA-level:"); for (const auto& p2xlregions : modified_region_xls_targets) { for (const auto& region : p2xlregions.second) @@ -5106,9 +5113,13 @@ static void scoreXLIons_( { progresslogger.startProgress(0, 1, "Generating decoys..."); ProteaseDigestion digestor; + const String enzyme = getStringOption_("peptide:enzyme"); digestor.setEnzyme(getStringOption_("peptide:enzyme")); digestor.setMissedCleavages(0); // for decoy generation disable missed cleavages + DecoyGenerator dg; + dg.setSeed(4711); + // append decoy proteins const size_t old_size = fasta_db.size(); for (size_t i = 0; i != old_size; ++i) @@ -5122,15 +5133,17 @@ static void scoreXLIons_( e.sequence = ""; for (const auto & aas : output) { - std::string s = aas.toUnmodifiedString(); - auto last = --s.end(); - std::reverse(s.begin(), last); + if (aas.size() <= 2) { e.sequence += aas.toUnmodifiedString(); continue; } + + //cout << "Seq. before reverse: " << s << endl; + //auto last = --s.end(); + //std::reverse(s.begin(), last); // standard peptide reverse + //cout << "Seq. after reverse : " << s << endl; // switch cleavage sites (like in Andromeda or DecoyPyrate) // if (s.size() >= 2) std::swap(s[s.size() - 1], s[s.size() - 2]); - e.sequence += s; + e.sequence += dg.shufflePeptides(aas, enzyme).toUnmodifiedString(); } - e.identifier = "DECOY_" + e.identifier; fasta_db.push_back(e); } @@ -5298,7 +5311,7 @@ static void scoreXLIons_( const int & isotope_error = l->second.second; const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); - float hyperScore(0), + float total_loss_score(0), tlss_MIC(0), tlss_err(0), tlss_Morph(0), @@ -5325,7 +5338,7 @@ static void scoreXLIons_( b_ions, y_ions, peak_matched, - hyperScore, + total_loss_score, tlss_MIC, tlss_Morph, tlss_modds, @@ -5335,7 +5348,10 @@ static void scoreXLIons_( ); const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - if (badTotalLossScore(hyperScore, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } + + total_loss_score = total_loss_score - 0.22 * (double)cit->size(); + + if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); @@ -5349,7 +5365,7 @@ static void scoreXLIons_( ah.err = tlss_err; ah.Morph = tlss_Morph; ah.modds = tlss_modds; - ah.total_loss_score = hyperScore; + ah.total_loss_score = total_loss_score; ah.immonium_score = im_MIC; ah.precursor_score = pc_MIC; ah.total_MIC = tlss_total_MIC; @@ -5582,7 +5598,7 @@ static void scoreXLIons_( partial_loss_sub_score = log1p(dot_product) + yFact + bFact; ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// */ - ah.total_loss_score = hyperScore; + ah.total_loss_score = hyperScore - 0.22 * (double)ah.sequence.size(); ah.MIC = tlss_MIC; ah.immonium_score = im_MIC; ah.precursor_score = pc_MIC; @@ -6238,6 +6254,7 @@ static void scoreXLIons_( sort(XL_FDR.begin(), XL_FDR.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters for (double xlFDR : XL_FDR) { + OPENMS_LOG_INFO << "Writing XL results at xl-FDR: " << xlFDR << endl; if (xlFDR > 0.0 && xlFDR < 1.0) { IDFilter::filterHitsByScore(xl_pi, xlFDR); @@ -6368,7 +6385,7 @@ static void scoreXLIons_( sort(XL_FDR.begin(), XL_FDR.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters for (double xlFDR : XL_FDR) { - + OPENMS_LOG_INFO << "Writing XL results at xl-FDR: " << xlFDR << endl; if (xlFDR > 0.0 && xlFDR < 1.0) { IDFilter::filterHitsByScore(xl_pi, xlFDR); From 64b3734165d45b72b8beb125e668849ca661b55b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 8 Dec 2020 19:16:09 +0100 Subject: [PATCH 147/471] tweak total loss score by sequence length --- src/utils/OpenNuXL.cpp | 88 +++++++++++++++++++++++++----------------- 1 file changed, 53 insertions(+), 35 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 384bfd75cb6..201a59ca374 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -422,6 +422,8 @@ class AnnotatedHit double explained_peak_fraction = 0; double wTop50 = 0; + size_t n_theoretical_peaks = 0; + static bool hasBetterScore(const AnnotatedHit& a, const AnnotatedHit& b) { return a.score > b.score; @@ -768,7 +770,8 @@ class OpenNuXL : float& modds, float& err, float& pc_MIC, - float& im_MIC) + float& im_MIC, + size_t& n_theoretical_peaks) { OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); @@ -783,7 +786,6 @@ class OpenNuXL : double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); - size_t comparisons(0); size_t matches(0); // maximum charge considered @@ -819,7 +821,7 @@ class OpenNuXL : peak_matched[index] = true; } } - ++comparisons; + ++n_theoretical_peaks; } } } @@ -856,7 +858,7 @@ class OpenNuXL : peak_matched[index] = true; } } - ++comparisons; + ++n_theoretical_peaks; } } @@ -983,7 +985,7 @@ class OpenNuXL : peak_matched[index] = true; } } - ++comparisons; + ++n_theoretical_peaks; } } pc_MIC /= TIC; @@ -1006,7 +1008,7 @@ class OpenNuXL : peak_matched[index] = true; } } - ++comparisons; + ++n_theoretical_peaks; }; // see DOI: 10.1021/pr3007045 A Systematic Investigation into the Nature of Tryptic HCD Spectra @@ -1082,7 +1084,7 @@ class OpenNuXL : exp_spectrum.back().getMZ(), (int)Morph); #else - modds = matchOddsScore_(comparisons, + modds = matchOddsScore_(n_theoretical_peaks, fragment_mass_tolerance_Da, exp_spectrum.size(), exp_spectrum.back().getMZ(), @@ -1111,7 +1113,8 @@ class OpenNuXL : float& plss_err, float& plss_modds, float& plss_pc_MIC, - float& plss_im_MIC) + float& plss_im_MIC, + size_t& n_theoretical_peaks) { OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); @@ -1140,7 +1143,6 @@ class OpenNuXL : double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 - size_t comparisons(0); size_t matches(0); // maximum charge considered @@ -1187,7 +1189,7 @@ class OpenNuXL : matches++; } } - ++comparisons; + ++n_theoretical_peaks; } } } @@ -1231,7 +1233,7 @@ class OpenNuXL : matches++; } } - ++comparisons; + ++n_theoretical_peaks; } } } @@ -1296,12 +1298,6 @@ class OpenNuXL : } #endif - - - - - - UInt y_ion_count(0), b_ion_count(0); double b_sum(0.0); for (Size i = 0; i != b_ions.size(); ++i) @@ -1374,7 +1370,7 @@ class OpenNuXL : matches++; } } - ++comparisons; + ++n_theoretical_peaks; } } } @@ -1399,7 +1395,7 @@ class OpenNuXL : matches++; } } - ++comparisons; + ++n_theoretical_peaks; }; static const double imY = EmpiricalFormula("C8H10NO").getMonoWeight(); @@ -1484,7 +1480,7 @@ class OpenNuXL : (int)plss_Morph); #else plss_modds = matchOddsScore_( - comparisons, + n_theoretical_peaks, fragment_mass_tolerance_Da, exp_spectrum.size(), exp_spectrum.back().getMZ(), @@ -1699,7 +1695,8 @@ static void scoreXLIons_( float &plss_Morph, float &plss_modds, float &plss_pc_MIC, - float &plss_im_MIC) + float &plss_im_MIC, + size_t &n_theoretical_peaks) { OPENMS_PRECONDITION(!partial_loss_template_z1_b_ions.empty(), "Empty partial loss spectrum provided."); OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); @@ -1717,6 +1714,9 @@ static void scoreXLIons_( marker_ions_sub_score_spectrum_z1, marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX]); marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; + + // count marker ions + n_theoretical_peaks += marker_ions_sub_score_spectrum_z1.size(); } scoreShiftedLadderIons_( @@ -1740,7 +1740,8 @@ static void scoreXLIons_( plss_err, plss_modds, plss_pc_MIC, - plss_im_MIC); + plss_im_MIC, + n_theoretical_peaks); #ifdef DEBUG_OpenNuXL LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif @@ -3428,6 +3429,7 @@ static void scoreXLIons_( variable_modifications.val.find(c_term_mod) != variable_modifications.val.end()) ++n_var_mods; ph.setMetaValue(String("variable_modifications"), n_var_mods); + ph.setMetaValue(String("n_theoretical_peaks"), ah.n_theoretical_peaks); // determine NA modification from index in map auto mod_combinations_it = mm.mod_combinations.cbegin(); @@ -3791,6 +3793,8 @@ static void scoreXLIons_( pc_MIC(0), im_MIC(0); + size_t n_theoretical_peaks(0); + vector intensity_sum(total_loss_template_z1_b_ions.size(), 0.0); vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); @@ -3816,7 +3820,8 @@ static void scoreXLIons_( tlss_modds, tlss_err, pc_MIC, - im_MIC + im_MIC, + n_theoretical_peaks ); const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); @@ -3848,7 +3853,7 @@ static void scoreXLIons_( ah.NA_mod_index = rna_mod_idx; ah.isotope_error = isotope_error; - + ah.n_theoretical_peaks = n_theoretical_peaks; auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); ah.ladder_score = ladderScore_(range) / (double)intensity_sum.size(); range = longestCompleteLadder_(intensity_sum.begin(), intensity_sum.end()); @@ -4347,6 +4352,7 @@ static void scoreXLIons_( bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + // not localized? annotate region if (best_localization < 0) { ModifiedRegion mr; @@ -4382,10 +4388,10 @@ static void scoreXLIons_( map aa2background_freq; // AA background distribution for normalization for (const ProteinIdentification& prot_id : prot_ids) - { + { const vector& phs = prot_id.getHits(); for (const ProteinHit& protein : phs) - { + { // for all identified proteins const String& acc = protein.getAccession(); bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); @@ -4398,7 +4404,7 @@ static void scoreXLIons_( auto mods = protein.getModifications(); - // count how many PSMs support XL-ed position in a protein + // count how many PSMs support XL-ed position in the current protein map position2psm_count; for (const auto& p2ms : mods.AALevelSummary) { @@ -5007,7 +5013,8 @@ static void scoreXLIons_( << "precursor_intensity_log10" << "NuXL:NA_MASS_z0" << "NuXL:NA_length" - << "nucleotide_mass_tags"; + << "nucleotide_mass_tags" + << "n_theoretical_peaks"; if (!purities.empty()) feature_set_ << "precursor_purity"; @@ -5318,6 +5325,7 @@ static void scoreXLIons_( tlss_modds(0), pc_MIC(0), im_MIC(0); + size_t n_theoretical_peaks(0); vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); @@ -5344,7 +5352,8 @@ static void scoreXLIons_( tlss_modds, tlss_err, pc_MIC, - im_MIC + im_MIC, + n_theoretical_peaks ); const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); @@ -5400,6 +5409,8 @@ static void scoreXLIons_( // combined score const double tags = exp_spectrum.getFloatDataArrays()[1][0]; ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); + ah.n_theoretical_peaks = n_theoretical_peaks; + //ah.score = OpenNuXL::calculateFastScore(ah); does this work too #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; @@ -5499,9 +5510,10 @@ static void scoreXLIons_( tlss_modds(0), partial_loss_sub_score(0), marker_ions_sub_score(0), - hyperScore(0), + total_loss_score(0), pc_MIC(0), im_MIC(0); + size_t n_theoretical_peaks(0); const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); @@ -5524,17 +5536,21 @@ static void scoreXLIons_( b_ions, y_ions, peak_matched, - hyperScore, + total_loss_score, tlss_MIC, tlss_Morph, tlss_modds, tlss_err, pc_MIC, - im_MIC + im_MIC, + n_theoretical_peaks ); const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - if (badTotalLossScore(hyperScore, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } + + total_loss_score = total_loss_score - 0.22 * (double)cit->size(); + + if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } vector intensity_xls(total_loss_template_z1_b_ions.size(), 0.0); @@ -5568,7 +5584,8 @@ static void scoreXLIons_( plss_Morph, plss_modds, plss_pc_MIC, - plss_im_MIC); + plss_im_MIC, + n_theoretical_peaks); const double total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)) + plss_MIC + (plss_pc_MIC - floor(plss_pc_MIC)) + plss_im_MIC + marker_ions_sub_score; @@ -5598,7 +5615,7 @@ static void scoreXLIons_( partial_loss_sub_score = log1p(dot_product) + yFact + bFact; ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// */ - ah.total_loss_score = hyperScore - 0.22 * (double)ah.sequence.size(); + ah.total_loss_score = total_loss_score; ah.MIC = tlss_MIC; ah.immonium_score = im_MIC; ah.precursor_score = pc_MIC; @@ -5647,6 +5664,7 @@ static void scoreXLIons_( // combined score const double tags = exp_spectrum.getFloatDataArrays()[1][0]; ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); + ah.n_theoretical_peaks = n_theoretical_peaks; #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; From de082a950f502b943240ef6df69283e2b4170532 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 9 Dec 2020 17:44:10 +0100 Subject: [PATCH 148/471] before cleanup --- .../METADATA/ProteinModificationSummary.h | 8 --- src/utils/OpenNuXL.cpp | 66 ++++++++++++++----- 2 files changed, 50 insertions(+), 24 deletions(-) diff --git a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h index 80a6e7d0543..8a810c4a75d 100644 --- a/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h +++ b/src/openms/include/OpenMS/METADATA/ProteinModificationSummary.h @@ -29,20 +29,12 @@ // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ -<<<<<<< HEAD -// $Authors: Timo Sachsenberg$ -======= // $Authors: Timo Sachsenberg $ ->>>>>>> upstream/feature/mod_statistic // -------------------------------------------------------------------------- #pragma once #include -<<<<<<< HEAD - -======= ->>>>>>> upstream/feature/mod_statistic #include namespace OpenMS diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 201a59ca374..d31e0c4043a 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -211,7 +211,18 @@ struct ImmoniumIonsInPeptide default: break; } } - } + } + + void swap() + { // swap entries for decoy generation + std::swap(Y,E); + std::swap(W,Q); + std::swap(F,M); + std::swap(H,K); + std::swap(C,L); + std::swap(P,L); + } + bool Y = false; bool W = false; bool F = false; @@ -1114,7 +1125,8 @@ class OpenNuXL : float& plss_modds, float& plss_pc_MIC, float& plss_im_MIC, - size_t& n_theoretical_peaks) + size_t& n_theoretical_peaks, + bool is_decoy) { OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); @@ -1696,7 +1708,8 @@ static void scoreXLIons_( float &plss_modds, float &plss_pc_MIC, float &plss_im_MIC, - size_t &n_theoretical_peaks) + size_t &n_theoretical_peaks, + bool is_decoy) { OPENMS_PRECONDITION(!partial_loss_template_z1_b_ions.empty(), "Empty partial loss spectrum provided."); OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); @@ -1741,7 +1754,8 @@ static void scoreXLIons_( plss_modds, plss_pc_MIC, plss_im_MIC, - n_theoretical_peaks); + n_theoretical_peaks, + is_decoy); #ifdef DEBUG_OpenNuXL LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif @@ -3826,7 +3840,7 @@ static void scoreXLIons_( const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - total_loss_score = total_loss_score - 0.22 * (double)sequence.size(); + //total_loss_score = total_loss_score - 0.22 * (double)sequence.size(); // early-out if super bad score if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { return; } @@ -4327,6 +4341,8 @@ static void scoreXLIons_( map> modified_region_xls_targets; map> modified_region_xls_decoys; + map name2mod; // used to free temporary residues + // store modification statistic for every protein for (const PeptideIdentification& pep : peps) { @@ -4336,10 +4352,21 @@ static void scoreXLIons_( const std::vector& ph_evidences = ph.getPeptideEvidences(); const int best_localization = ph.getMetaValue("NuXL:best_localization_position"); - // create a user defined modification - ResidueModification* xl = new ResidueModification(); - xl->setFullId(ph.getMetaValue("NuXL:NA")); // something not used in ResidueDB - xl->setOrigin('X'); // any AA + // create a user defined modification (at most once) + ResidueModification* xl; + const String NA = ph.getMetaValue("NuXL:NA"); + auto it = name2mod.find(NA); + if (it != name2mod.end()) + { + xl = it->second; + } + else + { + xl = new ResidueModification(); + xl->setFullId(NA); + xl->setOrigin('X'); // any AA + name2mod[NA] = xl; + } for (auto& ph_evidence : ph_evidences) { @@ -4374,7 +4401,7 @@ static void scoreXLIons_( if (xl_pos_in_protein < protein->getSequence().size()) { auto mods = protein->getModifications(); // TODO: add mutable reference access - mods.AALevelSummary[xl_pos_in_protein][*xl].count++; + mods.AALevelSummary[xl_pos_in_protein][xl].count++; protein->setModifications(mods); } } @@ -4478,7 +4505,7 @@ static void scoreXLIons_( { aa2psm_count_decoys[AA_at_position] += count; } - tsv_file.addLine(m2s.first.getFullId() + ":" + AA_at_position + String(position + 1) + "(" + String(count) + ")"); + tsv_file.addLine(m2s.first->getFullId() + ":" + AA_at_position + String(position + 1) + "(" + String(count) + ")"); } } @@ -4534,6 +4561,8 @@ static void scoreXLIons_( { tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second) + "\tfreq. normalized: " + String(a2p.second * aa2background_freq[a2p.first])); } + + for (auto m : name2mod) { delete(m.second); } // free memory } ExitCodes main_(int, const char**) override @@ -4939,7 +4968,7 @@ static void scoreXLIons_( FalseDiscoveryRate fdr; Param p = fdr.getParameters(); p.setValue("add_decoy_proteins", "true"); // we still want decoys in the result (e.g., to run percolator) - p.setValue("add_decoy_peptides", "true"); // we still want decoys in the result (e.g., to run percolator) + p.setValue("add_decoy_peptides", "true"); if (report_top_hits >= 2) { p.setValue("use_all_hits", "true"); @@ -5197,6 +5226,8 @@ static void scoreXLIons_( auto const & current_fasta_entry = fasta_db[fasta_index]; + bool is_decoy = current_fasta_entry.identifier.hasPrefix("DECOY_"); + digestor.digestUnmodified(current_fasta_entry.sequence, current_digest, min_peptide_length, max_peptide_length); for (auto cit = current_digest.begin(); cit != current_digest.end(); ++cit) @@ -5232,6 +5263,8 @@ static void scoreXLIons_( // determine which residues might give rise to an immonium ion ImmoniumIonsInPeptide iip(unmodified_sequence); + if (is_decoy) iip.swap(); + AASequence aas = AASequence::fromString(unmodified_sequence); ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications, aas); vector all_modified_peptides; @@ -5358,7 +5391,7 @@ static void scoreXLIons_( const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - total_loss_score = total_loss_score - 0.22 * (double)cit->size(); +// total_loss_score = total_loss_score - 0.22 * (double)cit->size(); if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } @@ -5548,7 +5581,7 @@ static void scoreXLIons_( const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - total_loss_score = total_loss_score - 0.22 * (double)cit->size(); +// total_loss_score = total_loss_score - 0.22 * (double)cit->size(); if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } @@ -5585,7 +5618,8 @@ static void scoreXLIons_( plss_modds, plss_pc_MIC, plss_im_MIC, - n_theoretical_peaks); + n_theoretical_peaks, + is_decoy); const double total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)) + plss_MIC + (plss_pc_MIC - floor(plss_pc_MIC)) + plss_im_MIC + marker_ions_sub_score; @@ -6317,7 +6351,7 @@ static void scoreXLIons_( << "-score_type" << "svm" << "-unitnorm" << "-post_processing_tdc" -// << "-nested_xval_bins" << "3" + << "-nested_xval_bins" << "3" << "-weights" << weights_out.toQString() << "-out_pin" << pin.toQString(); From 5ad7df328ec99f1ebe77174e00eb67103d779e9b Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Sat, 12 Dec 2020 09:45:22 +0100 Subject: [PATCH 149/471] disable quantile annotation --- src/utils/OpenNuXL.cpp | 1236 +++++++++++++++++++--------------------- 1 file changed, 600 insertions(+), 636 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index d31e0c4043a..3c7bfc3d18f 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -123,21 +123,17 @@ using namespace boost::accumulators; #endif //#define DEBUG_OpenNuXL 1 -//#define OPENNUXL_SEPARATE_FEATURES 1 -//#define DANGEROUS_FEAUTURES increases FDR on entrappment dataset //#define FILTER_BAD_SCORES_ID_TAGS filter out some good hits //#define FILTER_AMBIGIOUS_PEAKS so far only worse results //#define FILTER_NO_ARBITRARY_TAG_PRESENT #define CALCULATE_LONGEST_TAG //#define MODDS_ON_ABY_IONS_ONLY -//#define SVM_RECALIBRATE 1 //#define FILTER_RANKS 1 -//#define CALCULATE_NUCLEOTIDE_TAGS 1 #define DONT_ACCUMULATE_PARTIAL_ION_SCORES 1 #define CONSIDER_AA_LOSSES 1 -#define ANNOTATED_QUANTILES 1 +//#define ANNOTATED_QUANTILES 1 #ifdef ANNOTATED_QUANTILES typedef accumulator_set > quantile_accu_t; @@ -213,16 +209,6 @@ struct ImmoniumIonsInPeptide } } - void swap() - { // swap entries for decoy generation - std::swap(Y,E); - std::swap(W,Q); - std::swap(F,M); - std::swap(H,K); - std::swap(C,L); - std::swap(P,L); - } - bool Y = false; bool W = false; bool F = false; @@ -247,6 +233,7 @@ class AnnotatedHit StringView sequence; SignedSize peptide_mod_index = 0; // enumeration index of the non-NA peptide modification Size NA_mod_index = 0; // index of the NA modification + Size NA_adduct_amb_index = 0; // store index the entry in the set of ambiguous precursor adducts (e.g, C-NH3 vs. U-H2O) int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment @@ -431,6 +418,7 @@ class AnnotatedHit size_t tag_XLed = 0; // tag that contains the transition from unshifted to shifted double explained_peak_fraction = 0; + double matched_theo_fraction = 0; double wTop50 = 0; size_t n_theoretical_peaks = 0; @@ -820,13 +808,14 @@ class OpenNuXL : const Size exp_z = exp_charges[index]; // found peak match - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_DA = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_DA < max_dist_dalton) { if (!peak_matched[index]) { const double intensity = exp_spectrum[index].getIntensity(); dot_product += intensity; - b_mean_err += intensity * std::abs(theo_mz - exp_mz); + b_mean_err += intensity * abs_err_DA; b_ions[i] += intensity; ++matches; peak_matched[index] = true; @@ -852,17 +841,13 @@ class OpenNuXL : const Size exp_z = exp_charges[index]; // found peak match - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_DA = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_DA < max_dist_dalton) { - const double intensity = exp_spectrum[index].getIntensity(); - y_mean_err += intensity * std::abs(theo_mz - exp_mz); - dot_product += intensity; - y_ions[N-1 - i] += intensity; - if (!peak_matched[index]) { const double intensity = exp_spectrum[index].getIntensity(); - y_mean_err += intensity * std::abs(theo_mz - exp_mz); + y_mean_err += intensity * abs_err_DA; dot_product += intensity; y_ions[N-1 - i] += intensity; ++matches; @@ -888,7 +873,8 @@ class OpenNuXL : Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); const Size exp_z = exp_charges[index]; - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_DA = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_DA < max_dist_dalton) { if (!peak_matched[index]) { @@ -912,7 +898,8 @@ class OpenNuXL : Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); const Size exp_z = exp_charges[index]; - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_DA = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_DA < max_dist_dalton) { if (!peak_matched[index]) { @@ -1182,7 +1169,8 @@ class OpenNuXL : const Size exp_z = exp_charges[index]; // found peak match - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_Da = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_Da < max_dist_dalton) { if (!peak_matched[index]) { @@ -1194,7 +1182,7 @@ class OpenNuXL : } #endif const double intensity = exp_spectrum[index].getIntensity(); - b_mean_err += intensity * std::abs(theo_mz - exp_mz); + b_mean_err += intensity * abs_err_Da; dot_product += intensity; b_ions[i] += intensity; peak_matched[index] = true; @@ -1226,7 +1214,8 @@ class OpenNuXL : const Size exp_z = exp_charges[index]; // found peak match - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_Da = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_Da < max_dist_dalton) { if (!peak_matched[index]) { @@ -1238,7 +1227,7 @@ class OpenNuXL : } #endif const double intensity = exp_spectrum[index].getIntensity(); - y_mean_err += intensity * std::abs(theo_mz - exp_mz); + y_mean_err += intensity * abs_err_Da; dot_product += intensity; y_ions[N-1 - i] += intensity; peak_matched[index] = true; @@ -1269,7 +1258,8 @@ class OpenNuXL : Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); const Size exp_z = exp_charges[index]; - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_Da = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_Da < max_dist_dalton) { if (!peak_matched[index]) { @@ -1297,8 +1287,8 @@ class OpenNuXL : Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); const Size exp_z = exp_charges[index]; - - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_Da = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_Da < max_dist_dalton) { if (!peak_matched[index]) { @@ -1371,7 +1361,8 @@ class OpenNuXL : const Size exp_z = exp_charges[index]; // found peak match - if (exp_z == z && std::abs(theo_mz - exp_mz) < max_dist_dalton) + const double abs_err_Da = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_Da < max_dist_dalton) { if (!peak_matched[index]) { @@ -1925,6 +1916,7 @@ static void scoreXLIons_( struct RankScores { double explained_peak_fraction = 0; + size_t explained_peaks; double wTop50 = 0; }; @@ -1976,6 +1968,7 @@ static void scoreXLIons_( } r.wTop50 = log10(1.0 + sum_rank_diff); + r.explained_peaks = matched; r.explained_peak_fraction = matched / (double)spectrum.size(); return r; } @@ -2050,6 +2043,116 @@ static void scoreXLIons_( aa_plus_adduct_mass[m][r] = 0; } + ////////////////////// check if multiple AAs match to an adduct + // set of all possibly observable fragment adduct masses + map> res_adduct_mass2residue2adduct; + + map> adduct_mass2adduct_names; + + for (const auto & p : nucleotide_to_fragment_adducts) + { + for (const auto & fa : p.second) + { + adduct_mass2adduct_names[fa.mass].insert(fa.name); + for (const Residue* r : residues) + { + double m = fa.mass + r->getMonoWeight(Residue::Internal); // mass of residue + fragment adduct + res_adduct_mass2residue2adduct[m][r] = fa.name; // e.g. 432.1->'L'->'U-H2O' + } + } + } + + // 2 AA vs 1AA + adduct + for (const Residue* a : residues) + { + double am = a->getMonoWeight(Residue::Internal); + for (const Residue* b : residues) + { + double bm = b->getMonoWeight(Residue::Internal); + + // take 1000 Da as reference mass so we get meaningful Da from ppm + const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, am + bm + 1000.0) : fragment_mass_tolerance; + + // find all (shifted/normal) residues that match to an observed shift + auto left = res_adduct_mass2residue2adduct.lower_bound(am + bm - tolerance); + auto right = res_adduct_mass2residue2adduct.upper_bound(am + bm + tolerance); + for (; left != right; ++left) + { + auto& residues2adductname = left->second; + for (auto& r2s : residues2adductname) + { + cout << (am + bm) << ":" << a->getOneLetterCode() << b->getOneLetterCode() << "=" << r2s.first->getOneLetterCode() << "+" << r2s.second << endl; + } + } + } + } + + // 2 AA vs adduct (e.g., 2AA or same ion get's observed with and without adduct) + for (const Residue* a : residues) + { + double am = a->getMonoWeight(Residue::Internal); + for (const Residue* b : residues) + { + double bm = b->getMonoWeight(Residue::Internal); + + // take 1000 Da as reference mass so we get meaningful Da from ppm + const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, am + bm + 1000.0) : fragment_mass_tolerance; + + auto left = adduct_mass2adduct_names.lower_bound(am + bm - tolerance); + auto right = adduct_mass2adduct_names.upper_bound(am + bm + tolerance); + for (; left != right; ++left) + { + for (auto& name : left->second) + { + cout << (am + bm) << ":" << a->getOneLetterCode() << b->getOneLetterCode() << "=" << name << endl; + } + } + } + } + + // 1 (heavy) AA vs 1 (light) AA + adduct + for (const Residue* a : residues) + { + double am = a->getMonoWeight(Residue::Internal); + + // take 1000 Da as reference mass so we get meaningful Da from ppm + const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, am + 1000.0) : fragment_mass_tolerance; + + // find all (shifted/normal) residues that match to an observed shift + auto left = res_adduct_mass2residue2adduct.lower_bound(am - tolerance); + auto right = res_adduct_mass2residue2adduct.upper_bound(am + tolerance); + for (; left != right; ++left) + { + auto& residues2adductname = left->second; + for (auto& r2s : residues2adductname) + { + cout << am << ":" << a->getOneLetterCode() << "=" << r2s.first->getOneLetterCode() << "+" << r2s.second << endl; + } + } + } + + // 1 AA vs adduct (e.g., worst case an AA matches to an adduct) + for (const Residue* a : residues) + { + double am = a->getMonoWeight(Residue::Internal); + + // take 1000 Da as reference mass so we get meaningful Da from ppm + const float tolerance = fragment_mass_tolerance_unit_ppm ? Math::ppmToMass(fragment_mass_tolerance, am + 1000.0) : fragment_mass_tolerance; + + auto left = adduct_mass2adduct_names.lower_bound(am - tolerance); + auto right = adduct_mass2adduct_names.upper_bound(am + tolerance); + for (; left != right; ++left) + { + for (auto& name : left->second) + { + cout << am << ":" << a->getOneLetterCode() << "=" << name << endl; + } + } + } + + + //// + if (debug_level_ > 0) { // output ambigious masses @@ -2495,24 +2598,32 @@ static void scoreXLIons_( // determine NA on precursor from index in map auto mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, annotated_hits[scan_index][i].NA_mod_index); // advance to sum formula at index NA_mod_index - const String precursor_rna_adduct = *mod_combinations_it->second.begin(); // get first nucleotide formula e.g. UU-H2O TODO:is this correct? only handle the first????????????????????????????????????????????????????????????????????? - const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; - - if (precursor_rna_adduct == "none") - { - new_hits.push_back(annotated_hits[scan_index][i]); - } - else - { - // if we have a cross-link, copy PSM information for each cross-linkable nucleotides - for (auto const & c : feasible_MS2_adducts) + + const auto& NA_adducts = mod_combinations_it->second; // set of all NA adducts for current sum formula (e.g, U-H2O and C-NH3 have same elemental composition) + auto NA_adduct_it = mod_combinations_it->second.begin(); + for (size_t NA_adduct_amb_index = 0; NA_adduct_amb_index != NA_adducts.size(); ++NA_adduct_amb_index) + { // for all NA adducts with current sum formula (e.g, U-H2O and C-NH3) + const String& precursor_na_adduct = *NA_adduct_it; + const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_na_adduct).feasible_adducts; + + if (precursor_na_adduct == "none") { - AnnotatedHit a(annotated_hits[scan_index][i]); - a.cross_linked_nucleotide = c.first; // nucleotide - new_hits.push_back(a); + new_hits.push_back(annotated_hits[scan_index][i]); + } + else + { + // if we have a cross-link, copy PSM information for each cross-linkable nucleotides + for (auto const & c : feasible_MS2_adducts) + { + AnnotatedHit a(annotated_hits[scan_index][i]); + a.cross_linked_nucleotide = c.first; // nucleotide + a.NA_adduct_amb_index = NA_adduct_amb_index; + new_hits.push_back(a); + } } } } + annotated_hits[scan_index].swap(new_hits); } @@ -2536,52 +2647,57 @@ static void scoreXLIons_( // determine NA on precursor from index in map auto mod_combinations_it = mm.mod_combinations.begin(); std::advance(mod_combinations_it, ah.NA_mod_index); - const String precursor_rna_adduct = *mod_combinations_it->second.begin(); - const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; - const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; - const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); - if (precursor_rna_adduct == "none") - { - const double tags = exp[scan_index].getFloatDataArrays()[1][0]; - ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); - continue; - } + const auto& NA_adducts = mod_combinations_it->second; // set of all NA adducts for current sum formula (e.g, U-H2O and C-NH3 have same elemental composition) + auto NA_adduct_it = mod_combinations_it->second.begin(); + for (size_t NA_adduct_amb_index = 0; NA_adduct_amb_index != NA_adducts.size(); ++NA_adduct_amb_index, ++NA_adduct_it) + { // for all NA adducts with current sum formula (e.g, U-H2O and C-NH3) + const String& precursor_na_adduct = *NA_adduct_it; + const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_na_adduct).feasible_adducts; + const vector& marker_ions = all_feasible_adducts.at(precursor_na_adduct).marker_ions; + const double precursor_na_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); - // determine current nucleotide and associated partial losses - vector partial_loss_modification; - for (auto const & nuc_2_adducts : feasible_MS2_adducts) - { - if (nuc_2_adducts.first == ah.cross_linked_nucleotide) + if (precursor_na_adduct == "none") { - partial_loss_modification = nuc_2_adducts.second; + const double tags = exp[scan_index].getFloatDataArrays()[1][0]; + ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); + continue; + } + + // determine current nucleotide and associated partial losses + vector partial_loss_modification; + for (auto const & nuc_2_adducts : feasible_MS2_adducts) + { + if (nuc_2_adducts.first == ah.cross_linked_nucleotide) + { + partial_loss_modification = nuc_2_adducts.second; + } } - } - // TODO: not needed to generate all templates (but will make not much of a difference - // as this is only done a few thousand times during post-scoring). That way, - // the code is basically the same as in the main scoring loop. - PeakSpectrum partial_loss_template_z1, - partial_loss_template_z2, - partial_loss_template_z3; + // TODO: not needed to generate all templates (but will make not much of a difference + // as this is only done a few thousand times during post-scoring). That way, + // the code is basically the same as in the main scoring loop. + PeakSpectrum partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3; - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); - PeakSpectrum marker_ions_sub_score_spectrum_z1, - partial_loss_spectrum_z1, - partial_loss_spectrum_z2; + PeakSpectrum marker_ions_sub_score_spectrum_z1, + partial_loss_spectrum_z1, + partial_loss_spectrum_z2; - // nucleotide is associated with certain NA-related fragment losses? - if (!partial_loss_modification.empty()) - { - // shifted b- / y- / a-ions - // generate shifted_immonium_ions_sub_score_spectrum.empty - RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, + // nucleotide is associated with certain NA-related fragment losses? + if (!partial_loss_modification.empty()) + { + // shifted b- / y- / a-ions + // generate shifted_immonium_ions_sub_score_spectrum.empty + RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, current_peptide_mass_without_NA, - precursor_rna_adduct, - precursor_rna_mass, + precursor_na_adduct, + precursor_na_mass, 1, partial_loss_modification, partial_loss_template_z1, @@ -2589,37 +2705,37 @@ static void scoreXLIons_( partial_loss_template_z3, partial_loss_spectrum_z1); - RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, + RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, current_peptide_mass_without_NA, - precursor_rna_adduct, - precursor_rna_mass, + precursor_na_adduct, + precursor_na_mass, 2, // don't know the charge of the precursor at that point partial_loss_modification, partial_loss_template_z1, partial_loss_template_z2, partial_loss_template_z3, partial_loss_spectrum_z2); - } + } - // add shifted marker ions - marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation - RNPxlFragmentIonGenerator::addMS2MarkerIons( - marker_ions, - marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX], - marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); - - const PeakSpectrum& exp_spectrum = exp[scan_index]; - float partial_loss_sub_score(0), - marker_ions_sub_score(0), - plss_MIC(0), - plss_err(1.0), - plss_Morph(0), - plss_modds(0); + // add shifted marker ions + marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation + RNPxlFragmentIonGenerator::addMS2MarkerIons( + marker_ions, + marker_ions_sub_score_spectrum_z1, + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX], + marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); + + const PeakSpectrum& exp_spectrum = exp[scan_index]; + float partial_loss_sub_score(0), + marker_ions_sub_score(0), + plss_MIC(0), + plss_err(1.0), + plss_Morph(0), + plss_modds(0); //TODO: dieser Teil ist anders - postScorePartialLossFragments_( unmodified_sequence.size(), + postScorePartialLossFragments_( unmodified_sequence.size(), exp_spectrum, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, @@ -2634,21 +2750,23 @@ static void scoreXLIons_( plss_modds); - // fill in missing scores not considered in fast scoring - ah.pl_MIC = plss_MIC; - ah.pl_err = plss_err; - ah.pl_Morph = plss_Morph; - ah.pl_modds = plss_modds; + // fill in missing scores not considered in fast scoring + ah.pl_MIC = plss_MIC; + ah.pl_err = plss_err; + ah.pl_Morph = plss_Morph; + ah.pl_modds = plss_modds; // add extra matched ion current // TODO: dieser Teil ist anders - ah.total_MIC += plss_MIC + marker_ions_sub_score; - // scores from shifted peaks - ah.marker_ions_score = marker_ions_sub_score; - ah.partial_loss_score = partial_loss_sub_score; - // combined score - const double tags = exp[scan_index].getFloatDataArrays()[1][0]; - ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); - } + ah.total_MIC += plss_MIC + marker_ions_sub_score; + // scores from shifted peaks + ah.marker_ions_score = marker_ions_sub_score; + ah.partial_loss_score = partial_loss_sub_score; + // combined score + const double tags = exp[scan_index].getFloatDataArrays()[1][0]; + ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); + + } + } } } @@ -2711,17 +2829,17 @@ static void scoreXLIons_( // determine NA on precursor from index in map auto mod_combinations_it = mm.mod_combinations.cbegin(); std::advance(mod_combinations_it, a.NA_mod_index); - const String precursor_rna_adduct = *mod_combinations_it->second.begin(); // TODO: check if it is enough to consider only first precursor adduct ???????????????????????????????????????????????????????? - const double precursor_rna_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); + const String precursor_na_adduct = *mod_combinations_it->second.begin(); // TODO: check if it is enough to consider only first precursor adduct ???????????????????????????????????????????????????????? + const double precursor_na_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); // we don't localize on non-cross-links - if (precursor_rna_adduct == "none") { continue; } + if (precursor_na_adduct == "none") { continue; } // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum // 1. get all possible NA fragment shifts in the MS2 (based on the precursor RNA/DNA) - OPENMS_LOG_DEBUG << "Precursor NA adduct: " << precursor_rna_adduct << endl; + OPENMS_LOG_DEBUG << "Precursor NA adduct: " << precursor_na_adduct << endl; - const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_rna_adduct).feasible_adducts; + const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_na_adduct).feasible_adducts; if (feasible_MS2_adducts.empty()) { continue; } // should not be the case - check case of no nucleotide but base fragment ? @@ -2737,7 +2855,7 @@ static void scoreXLIons_( const vector& partial_loss_modification = nt_to_adducts->second; // get marker ions (these are not specific to the cross-linked nucleotide but also depend on the whole oligo bound to the precursor) - const vector& marker_ions = all_feasible_adducts.at(precursor_rna_adduct).marker_ions; + const vector& marker_ions = all_feasible_adducts.at(precursor_na_adduct).marker_ions; OPENMS_LOG_DEBUG << "Marker ions used for this Precursor NA adduct: " << endl; for (auto & fa : marker_ions) { @@ -2779,8 +2897,8 @@ static void scoreXLIons_( partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, fixed_and_variable_modified_peptide_weight, - precursor_rna_adduct, - precursor_rna_mass, + precursor_na_adduct, + precursor_na_mass, precursor_charge, partial_loss_modification, partial_loss_template_z1, @@ -3445,9 +3563,14 @@ static void scoreXLIons_( ph.setMetaValue(String("variable_modifications"), n_var_mods); ph.setMetaValue(String("n_theoretical_peaks"), ah.n_theoretical_peaks); - // determine NA modification from index in map + // determine empirical formula of NA modification from index in map auto mod_combinations_it = mm.mod_combinations.cbegin(); std::advance(mod_combinations_it, ah.NA_mod_index); + + // determine precursor + auto NA_adduct_it = mod_combinations_it->second.cbegin(); // set of all NA adducts for current sum formula (e.g, U-H2O and C-NH3 have same elemental composition) + std::advance(NA_adduct_it, ah.NA_adduct_amb_index); + ph.setMetaValue(String("NuXL:mass_error_p"), ah.mass_error_p); ph.setMetaValue(String("NuXL:total_loss_score"), ah.total_loss_score); ph.setMetaValue(String("NuXL:immonium_score"), ah.immonium_score); @@ -3475,8 +3598,8 @@ static void scoreXLIons_( ph.setMetaValue(String("NuXL:total_MIC"), ah.total_MIC); // fraction of matched ion current from total + partial losses - String NA = *mod_combinations_it->second.begin(); // TODO: consider only first (potentially ambigious one) ?????????????????????????????????????? - ph.setMetaValue(String("NuXL:NA"), NA); // return first nucleotide formula matching the index of the empirical formula + const String NA = *NA_adduct_it; + ph.setMetaValue(String("NuXL:NA"), NA); // the nucleotide formula e.g., U-H2O double na_mass_z0 = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); // NA uncharged mass via empirical formula // length of oligo @@ -3543,6 +3666,7 @@ static void scoreXLIons_( ph.setMetaValue("NuXL:aminoacid_id_to_max_tag_ratio", id2maxtag); ph.setMetaValue("nr_candidates", nr_candidates[scan_index]); ph.setMetaValue("NuXL:explained_peak_fraction", ah.explained_peak_fraction); + ph.setMetaValue("NuXL:theo_peak_fraction", ah.matched_theo_fraction); ph.setMetaValue("NuXL:wTop50", ah.wTop50); ph.setPeakAnnotations(ah.fragment_annotations); @@ -3677,41 +3801,6 @@ static void scoreXLIons_( search_parameters.precursor_mass_tolerance_ppm = getStringOption_("precursor:mass_tolerance_unit") == "ppm" ? true : false; search_parameters.fragment_mass_tolerance_ppm = getStringOption_("fragment:mass_tolerance_unit") == "ppm" ? true : false; search_parameters.digestion_enzyme = *ProteaseDB::getInstance()->getEnzyme(getStringOption_("peptide:enzyme")); - -#ifdef OPENNUXL_SEPARATE_FEATURES - for (auto & pi : peptide_ids) - { - for (auto & ph : pi.getHits()) - { - if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) - { - // fill XL related feature columns with zeros - for (const auto & s : feature_set_) - { - if (s.hasPrefix("NuXL")) ph.setMetaValue("XL_" + s, 0.0); - } - } - else // XL - { - // fill linear peptide releated feature columns with zero (after copying them over) - for (const auto& s : feature_set) - { - if (s.hasPrefix("NuXL")) - { - ph.setMetaValue("XL_" + s, static_cast(ph.getMetaValue(s))); - ph.setMetaValue(s, 0.0); - } - } - } - } - } - - // we duplicated the feature set - auto XL_columns = feature_set; - for (const auto& s : feature_set) { if (s.hasPrefix("NuXL")) XL_columns.push_back("XL_" + s); } - feature_set_ = XL_columns; -#endif - search_parameters.setMetaValue("feature_extractor", "TOPP_PSMFeatureExtractor"); search_parameters.setMetaValue("extra_features", ListUtils::concatenate(feature_set_, ",")); @@ -3780,7 +3869,7 @@ static void scoreXLIons_( const PeakSpectrum& exp_spectrum, const StringView sequence, const Size & mod_pep_idx, - const Size & rna_mod_idx, + const Size & na_mod_idx, const double & current_peptide_mass, const double & current_peptide_mass_without_NA, const double & exp_pc_mass, @@ -3840,8 +3929,6 @@ static void scoreXLIons_( const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - //total_loss_score = total_loss_score - 0.22 * (double)sequence.size(); - // early-out if super bad score if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { return; } @@ -3865,7 +3952,7 @@ static void scoreXLIons_( ah.total_MIC = tlss_total_MIC; - ah.NA_mod_index = rna_mod_idx; + ah.NA_mod_index = na_mod_idx; ah.isotope_error = isotope_error; ah.n_theoretical_peaks = n_theoretical_peaks; auto range = make_pair(intensity_sum.begin(), intensity_sum.end()); @@ -4681,7 +4768,8 @@ static void scoreXLIons_( << "-score_type" << "q-value" << "-post_processing_tdc" << "-weights" << weights_out.toQString() - << "-nested_xval_bins" << "3"; + << "-nested_xval_bins" << "3" + ; if (getStringOption_("peptide:enzyme") == "Lys-C") { @@ -5021,8 +5109,11 @@ static void scoreXLIons_( << "NuXL:aminoacid_id_to_max_tag_ratio" << "nr_candidates" << "NuXL:explained_peak_fraction" + << "NuXL:theo_peak_fraction" +#ifdef ANNOTATED_QUANTILES << "NuXL:QQ_TIC" << "NuXL:QQ_EXPLAINED_FRACTION" +#endif << "NuXL:wTop50" << "NuXL:marker_ions_score" @@ -5088,13 +5179,12 @@ static void scoreXLIons_( } progresslogger.startProgress(0, 1, "Filtering spectra..."); - const bool convert_to_single_charge = false; // whether to convert fragment peaks with isotopic patterns to single charge const double window_size = getDoubleOption_("window_size"); const size_t peak_count = getIntOption_("peak_count"); preprocessSpectra_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, - convert_to_single_charge, + false, // keep charge as is true, window_size, peak_count); // annotate charge progresslogger.endProgress(); @@ -5263,15 +5353,13 @@ static void scoreXLIons_( // determine which residues might give rise to an immonium ion ImmoniumIonsInPeptide iip(unmodified_sequence); - if (is_decoy) iip.swap(); - AASequence aas = AASequence::fromString(unmodified_sequence); ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications, aas); vector all_modified_peptides; ModifiedPeptideGenerator::applyVariableModifications(variable_modifications, aas, max_variable_mods_per_peptide, all_modified_peptides); for (SignedSize mod_pep_idx = 0; mod_pep_idx < (SignedSize)all_modified_peptides.size(); ++mod_pep_idx) - { + { // for all (modified) peptide sequences in the digest of the current protein const AASequence& fixed_and_variable_modified_peptide = all_modified_peptides[mod_pep_idx]; double current_peptide_mass_without_NA = fixed_and_variable_modified_peptide.getMonoWeight(); @@ -5284,12 +5372,12 @@ static void scoreXLIons_( // iterate over all NA sequences, calculate peptide mass and generate complete loss spectrum only once as this can potentially be reused Size NA_mod_index = 0; - for (std::map::const_iterator rna_mod_it = mm.formula2mass.begin(); - rna_mod_it != mm.formula2mass.end(); - ++rna_mod_it, ++NA_mod_index) + for (std::map::const_iterator na_mod_it = mm.formula2mass.begin(); + na_mod_it != mm.formula2mass.end(); + ++na_mod_it, ++NA_mod_index) { - const double precursor_rna_mass = rna_mod_it->second; - const double current_peptide_mass = current_peptide_mass_without_NA + precursor_rna_mass; // add NA mass + const double precursor_na_mass = na_mod_it->second; + const double current_peptide_mass = current_peptide_mass_without_NA + precursor_na_mass; // add NA mass // determine MS2 precursors that match to the current peptide mass MassToScanMultiMap::const_iterator low_it, up_it; @@ -5315,246 +5403,61 @@ static void scoreXLIons_( generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::ResidueType::YIon, total_loss_template_z1_y_ions); } + // retrieve NA adduct name + auto mod_combinations_it = mm.mod_combinations.begin(); + std::advance(mod_combinations_it, NA_mod_index); //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// // all ion scoring // if (!fast_scoring_) { - // retrieve NA adduct name - auto mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, NA_mod_index); - const String& precursor_rna_adduct = *mod_combinations_it->second.begin(); // TODO: check if sufficient to consider only first NA adduct here ????????????????????????????????????????????????????????????????????? - - if (precursor_rna_adduct == "none") - { - // score peptide without NA (same method as fast scoring) - for (auto & l = low_it; l != up_it; ++l) - { - const Size & scan_index = l->second.first; - const PeakSpectrum & exp_spectrum = spectra[scan_index]; - -#ifdef FILTER_NO_ARBITRARY_TAG_PRESENT - // require at least one mass tag - if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } -#endif + const auto& NA_adducts = mod_combinations_it->second; // set of all NA adducts for current sum formula (e.g, U-H2O and C-NH3 have same elemental composition) - // count candidate for spectrum -#ifdef _OPENMP - omp_set_lock(&(annotated_peptides_lock[scan_index])); - omp_set_lock(&(annotated_XLs_lock[scan_index])); - ++nr_candidates[scan_index]; - omp_unset_lock(&(annotated_XLs_lock[scan_index])); - omp_unset_lock(&(annotated_peptides_lock[scan_index])); -#endif - //const double exp_pc_mass = l->first; - const int & isotope_error = l->second.second; - const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); + auto NA_adduct_it = mod_combinations_it->second.begin(); + for (size_t NA_adduct_amb_index = 0; NA_adduct_amb_index != NA_adducts.size(); ++NA_adduct_amb_index, ++NA_adduct_it) + { // for all NA adducts with current sum formula (e.g, U-H2O and C-NH3) + const String& precursor_na_adduct = *NA_adduct_it; - float total_loss_score(0), - tlss_MIC(0), - tlss_err(0), - tlss_Morph(0), - tlss_modds(0), - pc_MIC(0), - im_MIC(0); - size_t n_theoretical_peaks(0); - - vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); - vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); - vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); - - vector peak_matched(exp_spectrum.size(), false); - scorePeptideIons_( - exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], - total_loss_template_z1_b_ions, - total_loss_template_z1_y_ions, - current_peptide_mass_without_NA, - exp_pc_charge, - iip, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - intensity_linear, - b_ions, - y_ions, - peak_matched, - total_loss_score, - tlss_MIC, - tlss_Morph, - tlss_modds, - tlss_err, - pc_MIC, - im_MIC, - n_theoretical_peaks - ); - - const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - -// total_loss_score = total_loss_score - 0.22 * (double)cit->size(); - - if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } - - const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; - const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); - - // add peptide hit - AnnotatedHit ah; - ah.mass_error_p = mass_error_score; - ah.sequence = *cit; // copy StringView - ah.peptide_mod_index = mod_pep_idx; - ah.MIC = tlss_MIC; - ah.err = tlss_err; - ah.Morph = tlss_Morph; - ah.modds = tlss_modds; - ah.total_loss_score = total_loss_score; - ah.immonium_score = im_MIC; - ah.precursor_score = pc_MIC; - ah.total_MIC = tlss_total_MIC; - - ah.NA_mod_index = NA_mod_index; - ah.isotope_error = isotope_error; - - auto range = make_pair(intensity_linear.begin(), intensity_linear.end()); - ah.ladder_score = ladderScore_(range) / (double)intensity_linear.size(); - range = longestCompleteLadder_(intensity_linear.begin(), intensity_linear.end()); - if (range.second != range.first) - { - ah.sequence_score = ladderScore_(range) / (double)intensity_linear.size(); - } - - RankScores rankscores = rankScores_(exp_spectrum, peak_matched); - ah.explained_peak_fraction = rankscores.explained_peak_fraction; - ah.wTop50 = rankscores.wTop50; - - // do we have at least one ladder peak -// const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, vector()); - - const XLTags longest_tags = getLongestABYLadderWithShift(b_ions, y_ions, vector(), vector()); - -#ifdef FILTER_BAD_SCORES_ID_TAGS - if (longest_tags.tag_unshifted == 0) continue; -#endif - ah.tag_XLed = longest_tags.tag_XLed; - ah.tag_unshifted = longest_tags.tag_unshifted; - ah.tag_shifted = longest_tags.tag_shifted; - - // combined score - const double tags = exp_spectrum.getFloatDataArrays()[1][0]; - ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); - ah.n_theoretical_peaks = n_theoretical_peaks; - //ah.score = OpenNuXL::calculateFastScore(ah); does this work too - -#ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; -#endif - -#ifdef _OPENMP - omp_set_lock(&(annotated_peptides_lock[scan_index])); -#endif - { -#ifdef ANNOTATED_QUANTILES - annotated_peptides_quantiles_peptides[scan_index](ah.total_loss_score); - - QQ_TIC[scan_index].insert(ah.total_MIC); - QQ_EXPLAINED_FRACTION[scan_index].insert(ah.explained_peak_fraction); -#endif - annotated_peptides[scan_index].emplace_back(move(ah)); - - // prevent vector from growing indefinitly (memory) but don't shrink the vector every time - if (annotated_peptides[scan_index].size() >= 2 * report_top_hits) - { - std::partial_sort(annotated_peptides[scan_index].begin(), annotated_peptides[scan_index].begin() + report_top_hits, annotated_peptides[scan_index].end(), AnnotatedHit::hasBetterScore); - annotated_peptides[scan_index].resize(report_top_hits); - } - } -#ifdef _OPENMP - omp_unset_lock(&(annotated_peptides_lock[scan_index])); -#endif - } - } - else // score peptide with NA MS1 adduct - { - // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum - // get NA fragment shifts in the MS2 (based on the precursor RNA/DNA) - auto const & all_NA_adducts = all_feasible_fragment_adducts.at(precursor_rna_adduct); - const vector& feasible_MS2_adducts = all_NA_adducts.feasible_adducts; - // get marker ions - const vector& marker_ions = all_NA_adducts.marker_ions; - - //cout << "'" << precursor_rna_adduct << "'" << endl; - //OPENMS_POSTCONDITION(!feasible_MS2_adducts.empty(), - // String("FATAL: No feasible adducts for " + precursor_rna_adduct).c_str()); - - - // Do we have (nucleotide) specific fragmentation adducts? for the current NA adduct on the precursor? - // If so, generate spectra for shifted ion series - - - // score individually for every nucleotide - for (auto const & nuc_2_adducts : feasible_MS2_adducts) + if (precursor_na_adduct == "none") { - // determine current nucleotide and associated partial losses - const char& cross_linked_nucleotide = nuc_2_adducts.first; - const vector& partial_loss_modification = nuc_2_adducts.second; - - PeakSpectrum marker_ions_sub_score_spectrum_z1; - // add shifted marker ions of charge 1 - marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation - RNPxlFragmentIonGenerator::addMS2MarkerIons( - marker_ions, - marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX], - marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); - - // nucleotide is associated with certain NA-related fragment losses? - vector partial_loss_template_z1_bions, partial_loss_template_z1_yions; - if (!partial_loss_modification.empty()) - { - generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::BIon, partial_loss_template_z1_bions); - generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::YIon, partial_loss_template_z1_yions); - } - + // score peptide without NA (same method as fast scoring) for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; const PeakSpectrum & exp_spectrum = spectra[scan_index]; - ////////////////////////////////////////// - // ID-Filter - if (skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) { continue; } -#ifdef FILTER_NO_ARBITRARY_TAG_PRESENT + + #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } -#endif + #endif -#ifdef _OPENMP + // count candidate for spectrum + #ifdef _OPENMP omp_set_lock(&(annotated_peptides_lock[scan_index])); omp_set_lock(&(annotated_XLs_lock[scan_index])); - // count candidate for spectrum ++nr_candidates[scan_index]; omp_unset_lock(&(annotated_XLs_lock[scan_index])); omp_unset_lock(&(annotated_peptides_lock[scan_index])); -#endif + #endif + //const double exp_pc_mass = l->first; const int & isotope_error = l->second.second; - float tlss_MIC(0), - tlss_err(1.0), - tlss_Morph(0), - tlss_modds(0), - partial_loss_sub_score(0), - marker_ions_sub_score(0), - total_loss_score(0), - pc_MIC(0), - im_MIC(0); + const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); + + float total_loss_score(0), + tlss_MIC(0), + tlss_err(0), + tlss_Morph(0), + tlss_modds(0), + pc_MIC(0), + im_MIC(0); size_t n_theoretical_peaks(0); - const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); + vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); + vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); + vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); - vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); vector peak_matched(exp_spectrum.size(), false); - vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); // b & a ions - vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); - scorePeptideIons_( exp_spectrum, exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], @@ -5566,7 +5469,7 @@ static void scoreXLIons_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, intensity_linear, - b_ions, + b_ions, y_ions, peak_matched, total_loss_score, @@ -5577,96 +5480,31 @@ static void scoreXLIons_( pc_MIC, im_MIC, n_theoretical_peaks - ); + ); const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - -// total_loss_score = total_loss_score - 0.22 * (double)cit->size(); + + // total_loss_score = total_loss_score - 0.22 * (double)cit->size(); if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } - vector intensity_xls(total_loss_template_z1_b_ions.size(), 0.0); - - vector b_xl_ions(b_ions.size(), 0.0); - vector y_xl_ions(b_ions.size(), 0.0); - - float plss_MIC(0), - plss_err(1.0), - plss_Morph(0), - plss_modds(0), - plss_pc_MIC(0), - plss_im_MIC(0); - - scoreXLIons_(partial_loss_modification, - iip, - exp_spectrum, - current_peptide_mass_without_NA, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - partial_loss_template_z1_bions, - partial_loss_template_z1_yions, - marker_ions_sub_score_spectrum_z1, - intensity_xls, - b_xl_ions, - y_xl_ions, - peak_matched, - partial_loss_sub_score, - marker_ions_sub_score, - plss_MIC, - plss_err, - plss_Morph, - plss_modds, - plss_pc_MIC, - plss_im_MIC, - n_theoretical_peaks, - is_decoy); - - const double total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)) + plss_MIC + (plss_pc_MIC - floor(plss_pc_MIC)) + plss_im_MIC + marker_ions_sub_score; - - // decreases number of hits (especially difficult cases - but also number of false discoveries) - if (filter_bad_partial_loss_scores && badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, (plss_pc_MIC - floor(plss_pc_MIC)), marker_ions_sub_score)) - { - continue; - } - const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); // add peptide hit AnnotatedHit ah; + ah.NA_adduct_amb_index = NA_adduct_amb_index; // store index the entry in the set of ambiguous precursor adducts ah.mass_error_p = mass_error_score; - ah.sequence = *cit; // copy StringView ah.peptide_mod_index = mod_pep_idx; -/* -/////////////////////////////////////////////////////////////////////////////// test recalculate hyperscore on merged XL/non-XL ladders - size_t y_ion_count = std::count_if(y_ions.begin(), y_ions.end(), [](double d) { return d > 1e-6; }); - size_t b_ion_count = std::count_if(b_ions.begin(), b_ions.end(), [](double d) { return d > 1e-6; }); - size_t dot_product = std::accumulate(intensity_xls.begin(), intensity_xls.end(), 0.0); - dot_product = std::accumulate(intensity_linear.begin(), intensity_linear.end(), dot_product); - const double yFact = logfactorial_(y_ion_count); - const double bFact = logfactorial_(b_ion_count); - partial_loss_sub_score = log1p(dot_product) + yFact + bFact; -////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// -*/ - ah.total_loss_score = total_loss_score; ah.MIC = tlss_MIC; - ah.immonium_score = im_MIC; - ah.precursor_score = pc_MIC; ah.err = tlss_err; ah.Morph = tlss_Morph; ah.modds = tlss_modds; - ah.pl_MIC = plss_MIC; - ah.pl_err = plss_err; - ah.pl_Morph = plss_Morph; - ah.pl_modds = plss_modds; - ah.pl_pc_MIC = plss_pc_MIC; - ah.pl_im_MIC = plss_im_MIC; - ah.cross_linked_nucleotide = cross_linked_nucleotide; - ah.total_MIC = total_MIC; - // scores from shifted peaks - ah.marker_ions_score = marker_ions_sub_score; - ah.partial_loss_score = partial_loss_sub_score; + ah.total_loss_score = total_loss_score; + ah.immonium_score = im_MIC; + ah.precursor_score = pc_MIC; + ah.total_MIC = tlss_total_MIC; ah.NA_mod_index = NA_mod_index; ah.isotope_error = isotope_error; @@ -5681,66 +5519,325 @@ static void scoreXLIons_( RankScores rankscores = rankScores_(exp_spectrum, peak_matched); ah.explained_peak_fraction = rankscores.explained_peak_fraction; + if (rankscores.explained_peaks > 0) ah.matched_theo_fraction = rankscores.explained_peaks / (float)n_theoretical_peaks; ah.wTop50 = rankscores.wTop50; + // do we have at least one ladder peak + // const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, vector()); - // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one -// const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, intensity_xls); - const XLTags longest_tags = getLongestABYLadderWithShift(b_ions, y_ions, b_xl_ions, y_xl_ions); + const XLTags longest_tags = getLongestABYLadderWithShift(b_ions, y_ions, vector(), vector()); -#ifdef FILTER_BAD_SCORES_ID_TAGS - if (longest_tags.tag_XLed == 0) { continue; } -#endif + #ifdef FILTER_BAD_SCORES_ID_TAGS + if (longest_tags.tag_unshifted == 0) continue; + #endif ah.tag_XLed = longest_tags.tag_XLed; ah.tag_unshifted = longest_tags.tag_unshifted; ah.tag_shifted = longest_tags.tag_shifted; // combined score const double tags = exp_spectrum.getFloatDataArrays()[1][0]; - ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); ah.n_theoretical_peaks = n_theoretical_peaks; + ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); + //ah.score = OpenNuXL::calculateFastScore(ah); does this work too -#ifdef DEBUG_OpenNuXL + #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; -#endif + #endif -#ifdef _OPENMP - omp_set_lock(&(annotated_XLs_lock[scan_index])); -#endif + #ifdef _OPENMP + omp_set_lock(&(annotated_peptides_lock[scan_index])); + #endif { -#ifdef ANNOTATED_QUANTILES - annotated_peptides_quantiles_XLs[scan_index](ah.total_loss_score + ah.partial_loss_score); + #ifdef ANNOTATED_QUANTILES + annotated_peptides_quantiles_peptides[scan_index](ah.total_loss_score); QQ_TIC[scan_index].insert(ah.total_MIC); QQ_EXPLAINED_FRACTION[scan_index].insert(ah.explained_peak_fraction); -#endif - annotated_XLs[scan_index].emplace_back(move(ah)); + #endif + annotated_peptides[scan_index].emplace_back(move(ah)); // prevent vector from growing indefinitly (memory) but don't shrink the vector every time - if (annotated_XLs[scan_index].size() >= 2 * report_top_hits) + if (annotated_peptides[scan_index].size() >= 2 * report_top_hits) { - std::partial_sort(annotated_XLs[scan_index].begin(), annotated_XLs[scan_index].begin() + report_top_hits, annotated_XLs[scan_index].end(), AnnotatedHit::hasBetterScore); - annotated_XLs[scan_index].resize(report_top_hits); + std::partial_sort(annotated_peptides[scan_index].begin(), annotated_peptides[scan_index].begin() + report_top_hits, annotated_peptides[scan_index].end(), AnnotatedHit::hasBetterScore); + annotated_peptides[scan_index].resize(report_top_hits); } } -#ifdef _OPENMP - omp_unset_lock(&(annotated_XLs_lock[scan_index])); -#endif + #ifdef _OPENMP + omp_unset_lock(&(annotated_peptides_lock[scan_index])); + #endif } - } // for every nucleotide in the precursor + } + else // score peptide with NA MS1 adduct + { + // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum + // get NA fragment shifts in the MS2 (based on the precursor RNA/DNA) + auto const & all_NA_adducts = all_feasible_fragment_adducts.at(precursor_na_adduct); + const vector& feasible_MS2_adducts = all_NA_adducts.feasible_adducts; + // get marker ions + const vector& marker_ions = all_NA_adducts.marker_ions; + + //cout << "'" << precursor_na_adduct << "'" << endl; + //OPENMS_POSTCONDITION(!feasible_MS2_adducts.empty(), + // String("FATAL: No feasible adducts for " + precursor_na_adduct).c_str()); + + + // Do we have (nucleotide) specific fragmentation adducts? for the current NA adduct on the precursor? + // If so, generate spectra for shifted ion series + + + // score individually for every nucleotide + for (auto const & nuc_2_adducts : feasible_MS2_adducts) + { + // determine current nucleotide and associated partial losses + const char& cross_linked_nucleotide = nuc_2_adducts.first; + const vector& partial_loss_modification = nuc_2_adducts.second; + + PeakSpectrum marker_ions_sub_score_spectrum_z1; + // add shifted marker ions of charge 1 + marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays().resize(1); // annotation + RNPxlFragmentIonGenerator::addMS2MarkerIons( + marker_ions, + marker_ions_sub_score_spectrum_z1, + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX], + marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); + + // nucleotide is associated with certain NA-related fragment losses? + vector partial_loss_template_z1_bions, partial_loss_template_z1_yions; + if (!partial_loss_modification.empty()) + { + generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::BIon, partial_loss_template_z1_bions); + generateTheoreticalMZsZ1_(fixed_and_variable_modified_peptide, Residue::YIon, partial_loss_template_z1_yions); + } + + for (auto & l = low_it; l != up_it; ++l) + { + const Size & scan_index = l->second.first; + const PeakSpectrum & exp_spectrum = spectra[scan_index]; + ////////////////////////////////////////// + // ID-Filter + if (skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) { continue; } + #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT + // require at least one mass tag + if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } + #endif + + #ifdef _OPENMP + omp_set_lock(&(annotated_peptides_lock[scan_index])); + omp_set_lock(&(annotated_XLs_lock[scan_index])); + // count candidate for spectrum + ++nr_candidates[scan_index]; + omp_unset_lock(&(annotated_XLs_lock[scan_index])); + omp_unset_lock(&(annotated_peptides_lock[scan_index])); + #endif + const int & isotope_error = l->second.second; + float tlss_MIC(0), + tlss_err(1.0), + tlss_Morph(0), + tlss_modds(0), + partial_loss_sub_score(0), + marker_ions_sub_score(0), + total_loss_score(0), + pc_MIC(0), + im_MIC(0); + size_t n_theoretical_peaks(0); + + const int & exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); + + vector intensity_linear(total_loss_template_z1_b_ions.size(), 0.0); + vector peak_matched(exp_spectrum.size(), false); + vector b_ions(total_loss_template_z1_b_ions.size(), 0.0); // b & a ions + vector y_ions(total_loss_template_z1_b_ions.size(), 0.0); + + scorePeptideIons_( + exp_spectrum, + exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + total_loss_template_z1_b_ions, + total_loss_template_z1_y_ions, + current_peptide_mass_without_NA, + exp_pc_charge, + iip, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + intensity_linear, + b_ions, + y_ions, + peak_matched, + total_loss_score, + tlss_MIC, + tlss_Morph, + tlss_modds, + tlss_err, + pc_MIC, + im_MIC, + n_theoretical_peaks + ); + + const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); + + // total_loss_score = total_loss_score - 0.22 * (double)cit->size(); + + if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } + + vector intensity_xls(total_loss_template_z1_b_ions.size(), 0.0); + + vector b_xl_ions(b_ions.size(), 0.0); + vector y_xl_ions(b_ions.size(), 0.0); + + float plss_MIC(0), + plss_err(1.0), + plss_Morph(0), + plss_modds(0), + plss_pc_MIC(0), + plss_im_MIC(0); + + scoreXLIons_(partial_loss_modification, + iip, + exp_spectrum, + current_peptide_mass_without_NA, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + partial_loss_template_z1_bions, + partial_loss_template_z1_yions, + marker_ions_sub_score_spectrum_z1, + intensity_xls, + b_xl_ions, + y_xl_ions, + peak_matched, + partial_loss_sub_score, + marker_ions_sub_score, + plss_MIC, + plss_err, + plss_Morph, + plss_modds, + plss_pc_MIC, + plss_im_MIC, + n_theoretical_peaks, + is_decoy); + + const double total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)) + plss_MIC + (plss_pc_MIC - floor(plss_pc_MIC)) + plss_im_MIC + marker_ions_sub_score; + + // decreases number of hits (especially difficult cases - but also number of false discoveries) + if (filter_bad_partial_loss_scores && badPartialLossScore(tlss_Morph, plss_Morph, plss_MIC, plss_im_MIC, (plss_pc_MIC - floor(plss_pc_MIC)), marker_ions_sub_score)) + { + continue; + } + + const double mass_error_ppm = (current_peptide_mass - l->first) / l->first * 1e6; + const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); + + // add peptide hit + AnnotatedHit ah; + ah.NA_adduct_amb_index = NA_adduct_amb_index; // store index the entry in the set of ambiguous precursor adducts + ah.mass_error_p = mass_error_score; + + ah.sequence = *cit; // copy StringView + ah.peptide_mod_index = mod_pep_idx; + /* + /////////////////////////////////////////////////////////////////////////////// test recalculate hyperscore on merged XL/non-XL ladders + size_t y_ion_count = std::count_if(y_ions.begin(), y_ions.end(), [](double d) { return d > 1e-6; }); + size_t b_ion_count = std::count_if(b_ions.begin(), b_ions.end(), [](double d) { return d > 1e-6; }); + size_t dot_product = std::accumulate(intensity_xls.begin(), intensity_xls.end(), 0.0); + dot_product = std::accumulate(intensity_linear.begin(), intensity_linear.end(), dot_product); + const double yFact = logfactorial_(y_ion_count); + const double bFact = logfactorial_(b_ion_count); + partial_loss_sub_score = log1p(dot_product) + yFact + bFact; + ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + */ + ah.total_loss_score = total_loss_score; + ah.MIC = tlss_MIC; + ah.immonium_score = im_MIC; + ah.precursor_score = pc_MIC; + ah.err = tlss_err; + ah.Morph = tlss_Morph; + ah.modds = tlss_modds; + ah.pl_MIC = plss_MIC; + ah.pl_err = plss_err; + ah.pl_Morph = plss_Morph; + ah.pl_modds = plss_modds; + ah.pl_pc_MIC = plss_pc_MIC; + ah.pl_im_MIC = plss_im_MIC; + ah.cross_linked_nucleotide = cross_linked_nucleotide; + ah.total_MIC = total_MIC; + // scores from shifted peaks + ah.marker_ions_score = marker_ions_sub_score; + ah.partial_loss_score = partial_loss_sub_score; + + ah.NA_mod_index = NA_mod_index; + ah.isotope_error = isotope_error; + + auto range = make_pair(intensity_linear.begin(), intensity_linear.end()); + ah.ladder_score = ladderScore_(range) / (double)intensity_linear.size(); + range = longestCompleteLadder_(intensity_linear.begin(), intensity_linear.end()); + if (range.second != range.first) + { + ah.sequence_score = ladderScore_(range) / (double)intensity_linear.size(); + } + + RankScores rankscores = rankScores_(exp_spectrum, peak_matched); + ah.explained_peak_fraction = rankscores.explained_peak_fraction; + if (rankscores.explained_peaks > 0) ah.matched_theo_fraction = rankscores.explained_peaks / (float)n_theoretical_peaks; + ah.wTop50 = rankscores.wTop50; + + + // does it have at least one shift from non-cross-linked AA to the neighboring cross-linked one + // const XLTags longest_tags = getLongestLadderWithShift(intensity_linear, intensity_xls); + const XLTags longest_tags = getLongestABYLadderWithShift(b_ions, y_ions, b_xl_ions, y_xl_ions); + + #ifdef FILTER_BAD_SCORES_ID_TAGS + if (longest_tags.tag_XLed == 0) { continue; } + #endif + ah.tag_XLed = longest_tags.tag_XLed; + ah.tag_unshifted = longest_tags.tag_unshifted; + ah.tag_shifted = longest_tags.tag_shifted; + + // combined score + const double tags = exp_spectrum.getFloatDataArrays()[1][0]; + ah.n_theoretical_peaks = n_theoretical_peaks; + ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); + + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << "best score in pre-score: " << score << endl; + #endif + + #ifdef _OPENMP + omp_set_lock(&(annotated_XLs_lock[scan_index])); + #endif + { + #ifdef ANNOTATED_QUANTILES + annotated_peptides_quantiles_XLs[scan_index](ah.total_loss_score + ah.partial_loss_score); + + QQ_TIC[scan_index].insert(ah.total_MIC); + QQ_EXPLAINED_FRACTION[scan_index].insert(ah.explained_peak_fraction); + #endif + annotated_XLs[scan_index].emplace_back(move(ah)); + + // prevent vector from growing indefinitly (memory) but don't shrink the vector every time + if (annotated_XLs[scan_index].size() >= 2 * report_top_hits) + { + std::partial_sort(annotated_XLs[scan_index].begin(), annotated_XLs[scan_index].begin() + report_top_hits, annotated_XLs[scan_index].end(), AnnotatedHit::hasBetterScore); + annotated_XLs[scan_index].resize(report_top_hits); + } + } + #ifdef _OPENMP + omp_unset_lock(&(annotated_XLs_lock[scan_index])); + #endif + } + } // for every nucleotide in the precursor + } } + } else // fast scoring { for (auto & l = low_it; l != up_it; ++l) { const Size & scan_index = l->second.first; - auto mod_combinations_it = mm.mod_combinations.begin(); - std::advance(mod_combinations_it, NA_mod_index); - const String& precursor_rna_adduct = *mod_combinations_it->second.begin(); // For fast scoring it should be sufficient to only consider any of the adducts for this mass and formula (e.g., C-H3N vs U-H2O) + const String& precursor_na_adduct = *mod_combinations_it->second.begin(); // For fast scoring it should be sufficient to only consider any of the adducts for this mass and formula (e.g., C-H3N vs U-H2O) MSSpectrum& exp_spectrum = spectra[scan_index]; - if (precursor_rna_adduct != "none" && skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) continue; + if (precursor_na_adduct != "none" && skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) continue; #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT @@ -5902,7 +5999,7 @@ static void scoreXLIons_( // annotate RNPxl related information to hits and create report vector csv_rows = RNPxlReport::annotate(spectra, peptide_ids, meta_values_to_export, marker_ions_tolerance); -#ifdef ANNOTATED_QUANTILES +#ifdef ANNOTATED_QUANTILES for (Size scan_index = 0; scan_index != peptide_ids.size(); ++scan_index) { PeptideIdentification& pi = peptide_ids[scan_index]; @@ -6039,7 +6136,8 @@ static void scoreXLIons_( for (const auto & ph : pi.getHits()) { const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - if (!is_XL || ph.getMetaValue("target_decoy") != "decoy") continue; + if (!is_XL) continue; // skip linear peptides as these don't have the XL values set + if (ph.getMetaValue("target_decoy") != "decoy") continue; double score = ph.getMetaValue(name); decoy_XL_scores.push_back(score); } @@ -6057,7 +6155,8 @@ static void scoreXLIons_( for (const auto & ph : pi.getHits()) { const bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - if (!is_XL) continue; + if (!is_XL) continue; // skip linear peptides as these don't have the XL values set + if (ph.getMetaValue("target_decoy") != "decoy") continue; double score = ph.getMetaValue(name); decoy_XL_scores.push_back(score); } @@ -6069,8 +6168,9 @@ static void scoreXLIons_( map medians; for (const String mn : { "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_err", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC" }) { -// medians[mn] = metaMedian(peptide_ids, mn); - medians[mn] = metaMean(peptide_ids, mn); + medians[mn] = metaMedian(peptide_ids, mn); + cout << "median(" << mn << "):" << medians[mn] << endl; + //medians[mn] = metaMean(peptide_ids, mn); } size_t imputed(0); @@ -6093,137 +6193,6 @@ static void scoreXLIons_( cout << "Imputed XL features in " << imputed << " linear peptides." << endl; } - -#ifdef SVM_RECALIBRATE - ///////////////////////////////////////// SVM score recalibration - // find size of minority class - map pep_t; - map pep_d; - map XL_t; - map XL_d; - - // map scores to index (sorted) - for (size_t index = 0; index != peptide_ids.size(); ++index) - { - if (peptide_ids[index].getHits().empty()) continue; - const PeptideHit& ph = peptide_ids[index].getHits()[0]; // get best match to current spectrum - bool is_target = ph.getMetaValue("target_decoy") == "target"; - bool is_XL = !(static_cast(ph.getMetaValue("NuXL:isXL")) == 0); - double score = ph.getScore(); - if (is_target) - { - if (is_XL) - { - XL_t[score] = index; - } - else - { - pep_t[score] = index; - } - } - else - { - if (is_XL) - { - XL_d[score] = index; - } - else - { - pep_d[score] = index; - } - } - } - size_t minority_class = std::min({pep_t.size(), pep_d.size(), XL_t.size(), XL_d.size()}); - cout << "Peptide (target/decoy)\t XL (target/decoy):" << endl; - cout << pep_t.size() << "\t" << pep_d.size() << "\t" << XL_t.size() << "\t" << XL_d.size() << endl; - - if (minority_class > 250) minority_class = 250; - - // keep only top elements (=highest scoring hits) for all classes - pep_t.erase(pep_t.begin(), next(pep_t.begin(), pep_t.size() - minority_class)); - pep_d.erase(pep_d.begin(), next(pep_d.begin(), pep_d.size() - minority_class)); - XL_t.erase(XL_t.begin(), next(XL_t.begin(), XL_t.size() - minority_class)); - XL_d.erase(XL_d.begin(), next(XL_d.begin(), XL_d.size() - minority_class)); - - // training indices = index of peptide id that correspond to top scoring hits (of the 4 classes) - set training_indices; - for (auto & l : {pep_t, pep_d, XL_t, XL_d}) - { - for (auto & i : l) training_indices.insert(i.second); - } - - if (minority_class > 100) - { - SimpleSVM::PredictorMap predictors; - map labels; - - // copy all scores in predictors ("score" + all from feature_set). - // Only add labels for balanced training set - size_t current_row(0); - for (size_t index = 0; index != peptide_ids.size(); ++index) - { - const vector& phits = peptide_ids[index].getHits(); - for (size_t psm_rank = 0; psm_rank != phits.size(); ++psm_rank) - { - const PeptideHit& ph = phits[psm_rank]; - bool is_target = ph.getMetaValue("target_decoy") == "target"; - double score = ph.getScore(); - // predictors["score"].push_back(score); - predictors["length"].push_back(ph.getSequence().size()); - for (auto & f : feature_set_) - { - double value = ph.getMetaValue(f); - predictors[f].push_back(value); - } - // only add label for training data (rank = 0 and previously selected for training) - if (psm_rank == 0 && training_indices.count(index) > 0) - { - labels[current_row] = is_target; - } - ++current_row; - } - } - - SimpleSVM svm; - Param svm_param = svm.getParameters(); - svm_param.setValue("kernel", "linear"); -// svm_param.setValue("kernel", "RBF"); -// svm_param.setValue("log2_C", ListUtils::create("0")); -// svm_param.setValue("log2_gamma", ListUtils::create("1")); - svm.setParameters(svm_param); - svm.setup(predictors, labels); - vector predictions; - cout << "Predicting class probabilities:" << endl; - svm.predict(predictions); - std::map feature_weights; - svm.getFeatureWeights(feature_weights); - /* - cout << "Feature weights:" << endl; - for (const auto& m : feature_weights) - { - cout << m.first << "\t" << m.second << endl; - } - cout << "Feature scaling:" << endl; - auto feature_scaling = svm.getScaling(); - for (const auto& m : feature_scaling) - { - cout << m.first << "\t" << m.second.first << "\t" << m.second.second << endl; - } -*/ - size_t psm_index(0); - for (size_t index = 0; index != peptide_ids.size(); ++index) - { - vector& phits = peptide_ids[index].getHits(); - for (size_t psm_rank = 0; psm_rank != phits.size(); ++psm_rank, ++psm_index) - { - PeptideHit& ph = phits[psm_rank]; - ph.setScore(predictions[psm_index].probabilities[1]); // set probability of being a target as score - } - peptide_ids[index].assignRanks(); - } - // IdXMLFile().store(out_idxml + "_svm.idXML", protein_ids, peptide_ids); - } -#endif fdr.apply(peptide_ids); // write ProteinIdentifications and PeptideIdentifications to IdXML @@ -6281,11 +6250,6 @@ static void scoreXLIons_( fdr.apply(xl_pi); fdr.apply(pep_pi); - if (debug_level_ > 1) - { - - } - IDFilter::removeDecoyHits(xl_pi); IDFilter::removeDecoyHits(pep_pi); From 254d03c450bf0829b44ed54104dedaed067469ea Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 15 Dec 2020 09:57:19 +0100 Subject: [PATCH 150/471] [FEATURE] remove interfering peaks from MS2 --- .../OpenMS/ANALYSIS/ID/PrecursorPurity.h | 5 +- .../source/ANALYSIS/ID/PrecursorPurity.cpp | 22 ++- .../ANALYSIS/XLMS/OpenPepXLAlgorithm.cpp | 2 +- .../ANALYSIS/XLMS/OpenPepXLLFAlgorithm.cpp | 2 +- src/utils/OpenNuXL.cpp | 175 ++++++++++++++++-- 5 files changed, 177 insertions(+), 29 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/ID/PrecursorPurity.h b/src/openms/include/OpenMS/ANALYSIS/ID/PrecursorPurity.h index 1f146f6927a..9ece6aba51d 100644 --- a/src/openms/include/OpenMS/ANALYSIS/ID/PrecursorPurity.h +++ b/src/openms/include/OpenMS/ANALYSIS/ID/PrecursorPurity.h @@ -67,7 +67,8 @@ namespace OpenMS double target_intensity = 0.0; double signal_proportion = 0.0; Size target_peak_count = 0; - Size residual_peak_count = 0; + Size interfering_peak_count = 0; + PeakSpectrum interfering_peaks; // interfering peaks }; /** @brief compute precursor purity metrics for each MS2 spectrum in a PeakMap @@ -77,7 +78,7 @@ namespace OpenMS * @param precursor_mass_tolerance The precursor tolerance. Is used for determining the targeted peak and deisotoping. * @param precursor_mass_tolerance_unit_ppm The unit of the precursor tolerance */ - static std::map computePrecursorPurities(const PeakMap& spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm); + static std::map computePrecursorPurities(const PeakMap& spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, bool ignore_missing_precursor_spectra = false); /** @brief compute precursor purity metrics for one MS2 precursor diff --git a/src/openms/source/ANALYSIS/ID/PrecursorPurity.cpp b/src/openms/source/ANALYSIS/ID/PrecursorPurity.cpp index 97b390aacc1..8bfb5977e0e 100644 --- a/src/openms/source/ANALYSIS/ID/PrecursorPurity.cpp +++ b/src/openms/source/ANALYSIS/ID/PrecursorPurity.cpp @@ -103,7 +103,7 @@ namespace OpenMS { target_intensity += isolated_window[next_iso_index].getIntensity(); - isolated_window.erase(isolated_window.begin()+next_iso_index); + isolated_window.erase(isolated_window.begin() + next_iso_index); target_peak_count++; } // always increment iso to progress the loop @@ -120,7 +120,8 @@ namespace OpenMS score.target_intensity = target_intensity; score.signal_proportion = rel_sig; score.target_peak_count = target_peak_count; - score.residual_peak_count = isolated_window.size(); + score.interfering_peak_count = isolated_window.size(); + score.interfering_peaks = isolated_window; return score; } @@ -135,18 +136,18 @@ namespace OpenMS score.signal_proportion = score.target_intensity / score.total_intensity; } score.target_peak_count = score1.target_peak_count + score2.target_peak_count; - score.residual_peak_count = score1.residual_peak_count + score2.residual_peak_count; + score.interfering_peak_count = score1.interfering_peak_count + score2.interfering_peak_count; return score; } - std::map PrecursorPurity::computePrecursorPurities(const PeakMap& spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm) + std::map PrecursorPurity::computePrecursorPurities(const PeakMap& spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, bool ignore_missing_precursor_spectra) { std::map purityscores; std::pair::iterator, bool> insert_return_value; int spectra_size = static_cast(spectra.size()); - if (spectra[0].getMSLevel() != 1) + if (spectra[0].getMSLevel() != 1 && !ignore_missing_precursor_spectra) { OPENMS_LOG_WARN << "Warning: Input data not suitable for Precursor Purity computation. First Spectrum is not MS1. Precursor Purity info will not be calculated!\n"; return purityscores; @@ -157,7 +158,7 @@ namespace OpenMS if (spectra[i].getMSLevel() == 2) { auto parent_spectrum_it = spectra.getPrecursorSpectrum(spectra.begin()+i); - if (parent_spectrum_it == spectra.end()) + if (parent_spectrum_it == spectra.end() && !ignore_missing_precursor_spectra) { OPENMS_LOG_WARN << "Warning: Input data not suitable for Precursor Purity computation. An MS2 spectrum without parent spectrum detected. Precursor Purity info will not be calculated!\n"; return std::map(); @@ -183,9 +184,12 @@ namespace OpenMS { if (spectra[i].getMSLevel() == 2) { - auto parent_spectrum_it = spectra.getPrecursorSpectrum(spectra.begin()+i); - PrecursorPurity::PurityScores score = PrecursorPurity::computePrecursorPurity((*parent_spectrum_it), spectra[i].getPrecursors()[0], precursor_mass_tolerance, precursor_mass_tolerance_unit_ppm); - + PrecursorPurity::PurityScores score; + auto parent_spectrum_it = spectra.getPrecursorSpectrum(spectra.begin() + i); + if (parent_spectrum_it != spectra.end()) + { + score = PrecursorPurity::computePrecursorPurity((*parent_spectrum_it), spectra[i].getPrecursors()[0], precursor_mass_tolerance, precursor_mass_tolerance_unit_ppm); + } #pragma omp critical (purityscores_access) { // replace the initialized values diff --git a/src/openms/source/ANALYSIS/XLMS/OpenPepXLAlgorithm.cpp b/src/openms/source/ANALYSIS/XLMS/OpenPepXLAlgorithm.cpp index 1d19646d4d7..18d8e87d4c6 100644 --- a/src/openms/source/ANALYSIS/XLMS/OpenPepXLAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/XLMS/OpenPepXLAlgorithm.cpp @@ -870,7 +870,7 @@ using namespace OpenMS; csm.precursor_target_intensity = precursor_purities[spectrum_light.getNativeID()].target_intensity; csm.precursor_signal_proportion = precursor_purities[spectrum_light.getNativeID()].signal_proportion; csm.precursor_target_peak_count = precursor_purities[spectrum_light.getNativeID()].target_peak_count; - csm.precursor_residual_peak_count = precursor_purities[spectrum_light.getNativeID()].residual_peak_count; + csm.precursor_residual_peak_count = precursor_purities[spectrum_light.getNativeID()].interfering_peak_count; } // num_iso_peaks array from deisotoping diff --git a/src/openms/source/ANALYSIS/XLMS/OpenPepXLLFAlgorithm.cpp b/src/openms/source/ANALYSIS/XLMS/OpenPepXLLFAlgorithm.cpp index bf0fb762d44..c1d4a8b674a 100644 --- a/src/openms/source/ANALYSIS/XLMS/OpenPepXLLFAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/XLMS/OpenPepXLLFAlgorithm.cpp @@ -788,7 +788,7 @@ using namespace OpenMS; csm.precursor_target_intensity = precursor_purities[spectrum.getNativeID()].target_intensity; csm.precursor_signal_proportion = precursor_purities[spectrum.getNativeID()].signal_proportion; csm.precursor_target_peak_count = precursor_purities[spectrum.getNativeID()].target_peak_count; - csm.precursor_residual_peak_count = precursor_purities[spectrum.getNativeID()].residual_peak_count; + csm.precursor_residual_peak_count = precursor_purities[spectrum.getNativeID()].interfering_peak_count; } // num_iso_peaks array from deisotoping diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 3c7bfc3d18f..c6750afae03 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -133,6 +133,8 @@ using namespace boost::accumulators; #define CONSIDER_AA_LOSSES 1 + + //#define ANNOTATED_QUANTILES 1 #ifdef ANNOTATED_QUANTILES @@ -141,6 +143,7 @@ typedef accumulator_set > quantile_accu_t; #include typedef accumulator_set > accumulator_t_quadratic; + struct SpectrumLevelScoreQuantiles { @@ -467,7 +470,7 @@ class OpenNuXL : protected: /// percolator feature set StringList feature_set_; - + void registerOptionsAndFlags_() override { registerInputFile_("in", "", "", "input file "); @@ -1139,6 +1142,34 @@ class OpenNuXL : }; #endif + auto ambigious_match = [&](const double& mz, const double z, const String& name)->bool + { + auto it = fragment_adduct2block_if_masses_present.find(name); // get vector of blocked mass lists + if (it != fragment_adduct2block_if_masses_present.end()) + { + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + for (auto ml : it->second) + { // for all blocked mass lists + bool mass_list_matches{true}; + for (const double m : ml) + { // for all masses in current mass list + Size index = exp_spectrum.findNearest(mz - m * z); + const double exp_mz = exp_spectrum[index].getMZ(); + + const double abs_err_Da = std::fabs(mz - m * z - exp_mz); + if (abs_err_Da >= max_dist_dalton) // no match? then this mass list is not ambigous (break and continue with next one) + { + mass_list_matches = false; + break; + } + } + if (mass_list_matches) { return true; } // mass list matched every peak -> ambigious explanation + } + } + return false; + }; + + double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 @@ -1154,12 +1185,19 @@ class OpenNuXL : { for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { - for (Size i = 0; i < partial_loss_template_z1_b_ions.size(); ++i) +////////////// !!!!!!!!!!!!!!!!!!!!!!!!! skip dangerous adduct because there is a tag with same mass + // TODO move out? + auto it = std::find(exp_spectrum.getStringDataArrays()[0].begin(), exp_spectrum.getStringDataArrays()[0].end(), fa.name); + bool has_tag_that_matches_fragmentadduct = (it != exp_spectrum.getStringDataArrays()[0].end()); + + for (Size i = 0; i < partial_loss_template_z1_b_ions.size(); ++i) { const double theo_mz = (partial_loss_template_z1_b_ions[i] + fa.mass + diff2b + (z-1) * Constants::PROTON_MASS_U) / z; + if (has_tag_that_matches_fragmentadduct && ambigious_match(theo_mz, z, fa.name)) continue; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak @@ -1200,6 +1238,10 @@ class OpenNuXL : { for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { +////////////// !!!!!!!!!!!!!!!!!!!!!!!!! skip dangerous adduct because there is a tag with same mass + auto it = std::find(exp_spectrum.getStringDataArrays()[0].begin(), exp_spectrum.getStringDataArrays()[0].end(), fa.name); + bool has_tag_that_matches_fragmentadduct = (it != exp_spectrum.getStringDataArrays()[0].end()); + for (Size i = 1; i < partial_loss_template_z1_y_ions.size(); ++i) // Note that we start at (i=1 -> y2) as trypsin would otherwise not cut at cross-linking site { const double theo_mz = (partial_loss_template_z1_y_ions[i] + fa.mass @@ -1207,6 +1249,8 @@ class OpenNuXL : const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + if (has_tag_that_matches_fragmentadduct && ambigious_match(theo_mz, z, fa.name)) continue; + // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak Size index = exp_spectrum.findNearest(theo_mz); @@ -1355,6 +1399,11 @@ class OpenNuXL : { const double theo_mz = (peptide_mass + fa.mass + z * Constants::PROTON_MASS_U) / z; + // TODO move out? + auto it = std::find(exp_spectrum.getStringDataArrays()[0].begin(), exp_spectrum.getStringDataArrays()[0].end(), fa.name); + bool has_tag_that_matches_fragmentadduct = (it != exp_spectrum.getStringDataArrays()[0].end()); + if (has_tag_that_matches_fragmentadduct && ambigious_match(theo_mz, z, fa.name)) continue; + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; Size index = exp_spectrum.findNearest(theo_mz); const double exp_mz = exp_spectrum[index].getMZ(); @@ -2008,6 +2057,8 @@ static void scoreXLIons_( #ifdef FILTER_AMBIGIOUS_PEAKS static map mass2high_frequency_; #endif + static map>> fragment_adduct2block_if_masses_present; + void calculateNucleotideTags_(PeakMap& exp, const double fragment_mass_tolerance, @@ -2062,6 +2113,9 @@ static void scoreXLIons_( } } + map> tag2ADs; + unordered_map> ADs2tag; + // 2 AA vs 1AA + adduct for (const Residue* a : residues) { @@ -2079,9 +2133,19 @@ static void scoreXLIons_( for (; left != right; ++left) { auto& residues2adductname = left->second; + const String& A = a->getOneLetterCode(); + const String& B = b->getOneLetterCode(); + const String tag = A+B; for (auto& r2s : residues2adductname) { - cout << (am + bm) << ":" << a->getOneLetterCode() << b->getOneLetterCode() << "=" << r2s.first->getOneLetterCode() << "+" << r2s.second << endl; + const String& adduct_name = r2s.second; + cout << (am + bm) << ":" << tag << "=" << r2s.first->getOneLetterCode() << "+" << adduct_name << endl; + tag2ADs[tag].insert(adduct_name); + ADs2tag[adduct_name].insert(tag); + vector list; + list.push_back(am); + list.push_back(bm); + fragment_adduct2block_if_masses_present[adduct_name].push_back(list); } } } @@ -2102,14 +2166,25 @@ static void scoreXLIons_( auto right = adduct_mass2adduct_names.upper_bound(am + bm + tolerance); for (; left != right; ++left) { - for (auto& name : left->second) + const String& A = a->getOneLetterCode(); + const String& B = b->getOneLetterCode(); + const String tag = A+B; + for (auto& adduct_name : left->second) { - cout << (am + bm) << ":" << a->getOneLetterCode() << b->getOneLetterCode() << "=" << name << endl; + cout << (am + bm) << ":" << tag << "=" << adduct_name << endl; + tag2ADs[tag].insert(adduct_name); + ADs2tag[adduct_name].insert(tag); + vector list; + list.push_back(am); + list.push_back(bm); + fragment_adduct2block_if_masses_present[adduct_name].push_back(list); } } } } + // The bad cases where one AA matches to one AA + adduct or even one AA to adduct + // 1 (heavy) AA vs 1 (light) AA + adduct for (const Residue* a : residues) { @@ -2124,9 +2199,16 @@ static void scoreXLIons_( for (; left != right; ++left) { auto& residues2adductname = left->second; + const String& A = a->getOneLetterCode(); for (auto& r2s : residues2adductname) { - cout << am << ":" << a->getOneLetterCode() << "=" << r2s.first->getOneLetterCode() << "+" << r2s.second << endl; + const String& adduct_name = r2s.second; + cout << am << ":" << A << "=" << r2s.first->getOneLetterCode() << "+" << adduct_name << endl; + tag2ADs[A].insert(adduct_name); + ADs2tag[adduct_name].insert(A); + vector list; + list.push_back(am); + fragment_adduct2block_if_masses_present[adduct_name].push_back(list); } } } @@ -2143,15 +2225,42 @@ static void scoreXLIons_( auto right = adduct_mass2adduct_names.upper_bound(am + tolerance); for (; left != right; ++left) { - for (auto& name : left->second) + const String& A = a->getOneLetterCode(); + for (auto& adduct_name : left->second) { - cout << am << ":" << a->getOneLetterCode() << "=" << name << endl; + cout << am << ":" << A << "=" << adduct_name << endl; + tag2ADs[A].insert(adduct_name); + ADs2tag[adduct_name].insert(A); + vector list; + list.push_back(am); + fragment_adduct2block_if_masses_present[adduct_name].push_back(list); } } } - - - //// +{ + OpenNuXLTagger tagger(0.03,1,2); + for (auto & spec : exp) + { + if (spec.getMSLevel() != 2) continue; + std::set tags; + tagger.getTag(spec, tags); + spec.getStringDataArrays().push_back({}); + for (const auto& s : tags) // map tag to ambigious fragment adduct and store + { + const auto it = tag2ADs.find(s); + if (it != tag2ADs.end()) + { + for (const auto& ad : it->second) + { + //cout << ad << " "; + spec.getStringDataArrays().back().push_back(ad); + } + } + }; +// cout << endl; + } +} + //////////////////////////////////// above should go into new function !!!!!!!!!!!!!!! as it is not nucleotide tag related if (debug_level_ > 0) { @@ -2400,7 +2509,8 @@ static void scoreXLIons_( bool single_charge_spectra, bool annotate_charge, double window_size, - size_t peakcount) + size_t peakcount, + const std::map& purities) { // filter MS2 map // remove 0 intensities @@ -2430,6 +2540,7 @@ static void scoreXLIons_( true); // add up intensities } + filterPeakInterference_(exp, purities); SqrtMower sqrt_mower_filter; sqrt_mower_filter.filterPeakMap(exp); @@ -4651,6 +4762,35 @@ static void scoreXLIons_( for (auto m : name2mod) { delete(m.second); } // free memory } + + void filterPeakInterference_(PeakMap& spectra, const map& purities, double fragment_mass_tolerance = 20.0, bool fragment_mass_tolerance_unit_ppm = true) + { + for (auto& s : spectra) + { + unordered_set idx_to_remove; + cout << s.getNativeID() << " " << purities.size() << endl; + auto it = purities.find(s.getNativeID()); + if (it != purities.end()) + { + for (const auto& interfering_peak : it->second.interfering_peaks) + { + const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? interfering_peak.getMZ() * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + auto pos = s.findNearest(interfering_peak.getMZ(), max_dist_dalton, max_dist_dalton); + if (pos != -1) + { + idx_to_remove.insert(pos); + } + } + vector idx_to_keep; // inverse + for (size_t i = 0; i != s.size(); ++i) + { // add indices we don't want to remove + if (idx_to_remove.find(i) == idx_to_remove.end()) idx_to_keep.push_back(i); + } + cout << "Filtered out " << idx_to_remove.size() << " peaks matching to precursor inference." << endl; + s.select(idx_to_keep); + } + } + } ExitCodes main_(int, const char**) override { @@ -5073,12 +5213,13 @@ static void scoreXLIons_( { PeakMap tmp_spectra; f.load(in_mzml, tmp_spectra); - int nMS1 = std::count_if(tmp_spectra.begin(), tmp_spectra.end(), [](MSSpectrum& s){return s.getMSLevel() == 1;}); + int nMS1 = std::count_if(tmp_spectra.begin(), tmp_spectra.end(), [](MSSpectrum& s){ return s.getMSLevel() == 1; }); + OPENMS_LOG_INFO << "Using " << nMS1 << " spectra for precursor purity calculation." << endl; if (nMS1 != 0) { // if isolation windows are properly annotated and correct if necessary checkAndCorrectIsolationWindows_(tmp_spectra); - purities = PrecursorPurity::computePrecursorPurities(tmp_spectra, precursor_mass_tolerance, precursor_mass_tolerance_unit_ppm); + purities = PrecursorPurity::computePrecursorPurities(tmp_spectra, precursor_mass_tolerance, precursor_mass_tolerance_unit_ppm, true); // true = ignore missing PCs } } // free spectra @@ -5185,7 +5326,7 @@ static void scoreXLIons_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, false, // keep charge as is - true, window_size, peak_count); // annotate charge + true, window_size, peak_count, purities); // annotate charge progresslogger.endProgress(); progresslogger.startProgress(0, 1, "Calculate Nucleotide Tags..."); @@ -5905,7 +6046,7 @@ static void scoreXLIons_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, false, // no single charge (false) - true, window_size, peak_count); // annotate charge (true) + true, window_size, peak_count, purities); // annotate charge (true) calculateNucleotideTags_(spectra, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, nucleotide_to_fragment_adducts); progresslogger.endProgress(); @@ -6535,6 +6676,8 @@ static void scoreXLIons_( map OpenNuXL::mass2high_frequency_ = {}; #endif +map>> OpenNuXL::fragment_adduct2block_if_masses_present = {}; + int main(int argc, const char** argv) { OpenNuXL tool; From ff35021098f4602ae3fee0c161912429fd600e56 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 17 Dec 2020 08:58:02 +0100 Subject: [PATCH 151/471] add b / y ion statistics --- .../OpenMS/ANALYSIS/RNPXL/MorpheusScore.h | 1 + .../ID/SimpleSearchEngineAlgorithm.cpp | 12 +-- .../source/ANALYSIS/RNPXL/HyperScore.cpp | 22 ++++- .../source/ANALYSIS/RNPXL/MorpheusScore.cpp | 7 ++ .../openms/source/PrecursorPurity_test.cpp | 20 ++--- src/utils/OpenNuXL.cpp | 85 +++++++++++-------- 6 files changed, 94 insertions(+), 53 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/MorpheusScore.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/MorpheusScore.h index 63335f20bed..14ce8fe0a7d 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/MorpheusScore.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/MorpheusScore.h @@ -58,6 +58,7 @@ struct OPENMS_DLLAPI MorpheusScore float MIC = 0; ///< ion current of matches (experimental peaks) float TIC = 0; ///< total ion current (experimental peak) float err = 0; ///< average absolute mass error of matched fragments (in Da) + float err_ppm = 0; ///< average absolute mass error of matched fragments (in ppm) }; /// returns Morpheus Score, \#matched ions, \#total ions, \#matched intensities, \#total fragment intensities (TIC) diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index 557dffd1cf1..f1e6068fbea 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -93,7 +93,7 @@ namespace OpenMS precursor_mass_tolerance_unit_valid_strings.push_back("ppm"); precursor_mass_tolerance_unit_valid_strings.push_back("Da"); - defaults_.setValue("precursor:mass_tolerance_unit", "ppm", "Unit of precursor mass tolerance."); + defaults_.setValue("precursor:mass_tolerance_unit", "ppm", "Unit of precursor mass tolerance +/- to the theoretical one."); defaults_.setValidStrings("precursor:mass_tolerance_unit", precursor_mass_tolerance_unit_valid_strings); defaults_.setValue("precursor:min_charge", 2, "Minimum precursor charge to be considered."); @@ -105,7 +105,7 @@ namespace OpenMS IntList isotopes = {0, 1}; defaults_.setValue("precursor:isotopes", isotopes, "Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak)"); - defaults_.setValue("fragment:mass_tolerance", 10.0, "Fragment mass tolerance"); + defaults_.setValue("fragment:mass_tolerance", 10.0, "Fragment mass tolerance +/- to the theoretical one"); StringList fragment_mass_tolerance_unit_valid_strings; fragment_mass_tolerance_unit_valid_strings.push_back("ppm"); @@ -593,13 +593,13 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, if (precursor_mass_tolerance_unit_ppm) // ppm { - low_it = multimap_mass_2_scan_index.lower_bound(current_peptide_mass - 0.5 * current_peptide_mass * precursor_mass_tolerance_ * 1e-6); - up_it = multimap_mass_2_scan_index.upper_bound(current_peptide_mass + 0.5 * current_peptide_mass * precursor_mass_tolerance_ * 1e-6); + low_it = multimap_mass_2_scan_index.lower_bound(current_peptide_mass - current_peptide_mass * precursor_mass_tolerance_ * 1e-6); + up_it = multimap_mass_2_scan_index.upper_bound(current_peptide_mass + current_peptide_mass * precursor_mass_tolerance_ * 1e-6); } else // Dalton { - low_it = multimap_mass_2_scan_index.lower_bound(current_peptide_mass - 0.5 * precursor_mass_tolerance_); - up_it = multimap_mass_2_scan_index.upper_bound(current_peptide_mass + 0.5 * precursor_mass_tolerance_); + low_it = multimap_mass_2_scan_index.lower_bound(current_peptide_mass - precursor_mass_tolerance_); + up_it = multimap_mass_2_scan_index.upper_bound(current_peptide_mass + precursor_mass_tolerance_); } // no matching precursor in data diff --git a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp index 15f271c43a3..892b90f23a3 100644 --- a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp @@ -125,7 +125,13 @@ namespace OpenMS return hyperScore; } - double HyperScore::computeWithDetail(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum, PSMDetail& d) + double HyperScore::computeWithDetail(double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const PeakSpectrum& exp_spectrum, + const PeakSpectrum& theo_spectrum, + std::vector& b_ions, + std::vector& y_ions, + PSMDetail& d) { if (exp_spectrum.size() < 1 || theo_spectrum.size() < 1) { @@ -133,6 +139,12 @@ namespace OpenMS return 0.0; } + bool store_ion_intensities = true; + if (b_ions.empty() || y_ions.empty()) + { + store_ion_intensities = false; + } + // TODO this assumes only one StringDataArray is present and it is the right one const PeakSpectrum::StringDataArray* ion_names; if (theo_spectrum.getStringDataArrays().size() > 0) @@ -154,8 +166,12 @@ namespace OpenMS MatchedIterator it(theo_spectrum, exp_spectrum, fragment_mass_tolerance); for (; it != it.end(); ++it) { - abs_error += Math::getPPMAbs((*it).getMZ(), it.ref().getMZ()); - dot_product += (*it).getIntensity() * it.ref().getIntensity(); /* * mass_error */; + const double exp_mz{it.ref().getMZ()}; + const double theo_mz{(*it).getMZ()}; + const double exp_int{it.ref().getIntensity()}; + const double theo_int{(*it).getIntensity()}; + abs_error += Math::getPPMAbs(theo, exp_mz); + dot_product += theo_int * exp_int; /* * mass_error */; // fragment annotations in XL-MS data are more complex and do not start with the ion type, but the ion type always follows after a $ auto i = it.refIdx(); if ((*ion_names)[i][0] == 'y' || (*ion_names)[i].hasSubstring("$y")) diff --git a/src/openms/source/ANALYSIS/RNPXL/MorpheusScore.cpp b/src/openms/source/ANALYSIS/RNPXL/MorpheusScore.cpp index 225d11674f0..b75a2f2aacf 100644 --- a/src/openms/source/ANALYSIS/RNPXL/MorpheusScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/MorpheusScore.cpp @@ -34,6 +34,7 @@ #include #include +#include #include namespace OpenMS @@ -83,6 +84,7 @@ namespace OpenMS e = 0; double match_intensity(0.0); double sum_error(0.0); + double sum_error_ppm(0.0); while (t < n_t && e < n_e) { @@ -94,6 +96,7 @@ namespace OpenMS { match_intensity += exp_spectrum[e].getIntensity(); sum_error += fabs(d); + sum_error_ppm += Math::getPPMAbs(exp_mz, theo_mz); ++e; // sum up experimental peak intensity only once } else if (d < 0) // exp. peak is left of theo. peak (outside of tolerance window) @@ -114,6 +117,7 @@ namespace OpenMS psm.MIC = match_intensity; psm.TIC = total_intensity; psm.err = matches > 0 ? sum_error / static_cast(matches) : 1e10; + psm.err_ppm = matches > 0 ? sum_error_ppm / static_cast(matches) : 1e10; return psm; } @@ -170,6 +174,7 @@ namespace OpenMS e = 0; double match_intensity(0.0); double sum_error(0.0); + double sum_error_ppm(0.0); while (t < n_t && e < n_e) { @@ -185,6 +190,7 @@ namespace OpenMS { match_intensity += exp_spectrum[e].getIntensity(); sum_error += fabs(d); + sum_error_ppm += Math::getPPMAbs(exp_mz, theo_mz); } ++e; // sum up experimental peak intensity only once } @@ -206,6 +212,7 @@ namespace OpenMS psm.MIC = match_intensity; psm.TIC = total_intensity; psm.err = matches > 0 ? sum_error / static_cast(matches) : 1e10; + psm.err_ppm = matches > 0 ? sum_error_ppm / static_cast(matches) : 1e10; return psm; } diff --git a/src/tests/class_tests/openms/source/PrecursorPurity_test.cpp b/src/tests/class_tests/openms/source/PrecursorPurity_test.cpp index 3e01854bb52..bb7a9cda5b4 100644 --- a/src/tests/class_tests/openms/source/PrecursorPurity_test.cpp +++ b/src/tests/class_tests/openms/source/PrecursorPurity_test.cpp @@ -68,7 +68,7 @@ START_SECTION(static PurityScores computePrecursorPurity(const PeakSpectrum& ms1 TEST_REAL_SIMILAR(score.target_intensity, 8923915) TEST_REAL_SIMILAR(score.signal_proportion, 0.77211) TEST_EQUAL(score.target_peak_count, 1) - TEST_EQUAL(score.residual_peak_count, 3) + TEST_EQUAL(score.interfering_peak_count, 3) pre = spectra[3].getPrecursors()[0]; score = PrecursorPurity::computePrecursorPurity(spectra[0], pre, 0.2, false); @@ -76,7 +76,7 @@ START_SECTION(static PurityScores computePrecursorPurity(const PeakSpectrum& ms1 TEST_REAL_SIMILAR(score.target_intensity, 7057944) TEST_REAL_SIMILAR(score.signal_proportion, 0.77573) TEST_EQUAL(score.target_peak_count, 1) - TEST_EQUAL(score.residual_peak_count, 4) + TEST_EQUAL(score.interfering_peak_count, 4) END_SECTION @@ -91,51 +91,51 @@ START_SECTION(static computePrecursorPurities(const PeakMap& spectra, double pre TEST_REAL_SIMILAR(purityscores[spectra[0].getNativeID()].target_intensity, 0) TEST_REAL_SIMILAR(purityscores[spectra[0].getNativeID()].signal_proportion, 0) TEST_EQUAL(purityscores[spectra[0].getNativeID()].target_peak_count, 0) - TEST_EQUAL(purityscores[spectra[0].getNativeID()].residual_peak_count, 0) + TEST_EQUAL(purityscores[spectra[0].getNativeID()].interfering_peak_count, 0) // 5 MS2 spectra between two MS1 spectra TEST_REAL_SIMILAR(purityscores[spectra[1].getNativeID()].total_intensity, 5517171) TEST_REAL_SIMILAR(purityscores[spectra[1].getNativeID()].target_intensity, 5517171) TEST_REAL_SIMILAR(purityscores[spectra[1].getNativeID()].signal_proportion, 1) TEST_EQUAL(purityscores[spectra[1].getNativeID()].target_peak_count, 1) - TEST_EQUAL(purityscores[spectra[1].getNativeID()].residual_peak_count, 0) + TEST_EQUAL(purityscores[spectra[1].getNativeID()].interfering_peak_count, 0) TEST_REAL_SIMILAR(purityscores[spectra[2].getNativeID()].total_intensity, 11287967.625) TEST_REAL_SIMILAR(purityscores[spectra[2].getNativeID()].target_intensity, 7390478.5) TEST_REAL_SIMILAR(purityscores[spectra[2].getNativeID()].signal_proportion, 0.65472) TEST_EQUAL(purityscores[spectra[2].getNativeID()].target_peak_count, 1) - TEST_EQUAL(purityscores[spectra[2].getNativeID()].residual_peak_count, 3) + TEST_EQUAL(purityscores[spectra[2].getNativeID()].interfering_peak_count, 3) TEST_REAL_SIMILAR(purityscores[spectra[3].getNativeID()].total_intensity, 9098343.89062) TEST_REAL_SIMILAR(purityscores[spectra[3].getNativeID()].target_intensity, 7057944) TEST_REAL_SIMILAR(purityscores[spectra[3].getNativeID()].signal_proportion, 0.77573) TEST_EQUAL(purityscores[spectra[3].getNativeID()].target_peak_count, 1) - TEST_EQUAL(purityscores[spectra[3].getNativeID()].residual_peak_count, 4) + TEST_EQUAL(purityscores[spectra[3].getNativeID()].interfering_peak_count, 4) TEST_REAL_SIMILAR(purityscores[spectra[4].getNativeID()].total_intensity, 9762418.03906) TEST_REAL_SIMILAR(purityscores[spectra[4].getNativeID()].target_intensity, 7029896.5) TEST_REAL_SIMILAR(purityscores[spectra[4].getNativeID()].signal_proportion, 0.72009) TEST_EQUAL(purityscores[spectra[4].getNativeID()].target_peak_count, 1) - TEST_EQUAL(purityscores[spectra[4].getNativeID()].residual_peak_count, 5) + TEST_EQUAL(purityscores[spectra[4].getNativeID()].interfering_peak_count, 5) TEST_REAL_SIMILAR(purityscores[spectra[5].getNativeID()].total_intensity, 5465177) TEST_REAL_SIMILAR(purityscores[spectra[5].getNativeID()].target_intensity, 5465177) TEST_REAL_SIMILAR(purityscores[spectra[5].getNativeID()].signal_proportion, 1) TEST_EQUAL(purityscores[spectra[5].getNativeID()].target_peak_count, 1) - TEST_EQUAL(purityscores[spectra[5].getNativeID()].residual_peak_count, 0) + TEST_EQUAL(purityscores[spectra[5].getNativeID()].interfering_peak_count, 0) // using the ID of an MS1 spectrum, a new ID for the map, adds a new Score to the map, initialized to 0 TEST_REAL_SIMILAR(purityscores[spectra[6].getNativeID()].total_intensity, 0) TEST_REAL_SIMILAR(purityscores[spectra[6].getNativeID()].target_intensity, 0) TEST_REAL_SIMILAR(purityscores[spectra[6].getNativeID()].signal_proportion, 0) TEST_EQUAL(purityscores[spectra[6].getNativeID()].target_peak_count, 0) - TEST_EQUAL(purityscores[spectra[6].getNativeID()].residual_peak_count, 0) + TEST_EQUAL(purityscores[spectra[6].getNativeID()].interfering_peak_count, 0) TEST_REAL_SIMILAR(purityscores["randomString"].total_intensity, 0) TEST_REAL_SIMILAR(purityscores["randomString"].target_intensity, 0) TEST_REAL_SIMILAR(purityscores["randomString"].signal_proportion, 0) TEST_EQUAL(purityscores["randomString"].target_peak_count, 0) - TEST_EQUAL(purityscores["randomString"].residual_peak_count, 0) + TEST_EQUAL(purityscores["randomString"].interfering_peak_count, 0) PeakMap spectra_copy = spectra; diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index c6750afae03..0e3a9c9e3f4 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -343,7 +343,7 @@ class AnnotatedHit Morph: number of matched peaks + the fraction of MIC */ float pl_MIC = 0; - float pl_err = 0; + float pl_err = 0.0; float pl_Morph = 0; /* @@ -811,14 +811,17 @@ class OpenNuXL : const Size exp_z = exp_charges[index]; // found peak match - const double abs_err_DA = std::abs(theo_mz - exp_mz); - if (exp_z == z && abs_err_DA < max_dist_dalton) + const double abs_err_Da = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_Da < max_dist_dalton) { if (!peak_matched[index]) { const double intensity = exp_spectrum[index].getIntensity(); dot_product += intensity; - b_mean_err += intensity * abs_err_DA; + if (b_ions[i] == 0) // only b-ion mass error otherwise counts don't match for mean err calculation + { + b_mean_err += Math::getPPMAbs(exp_mz, theo_mz); + } b_ions[i] += intensity; ++matches; peak_matched[index] = true; @@ -844,13 +847,13 @@ class OpenNuXL : const Size exp_z = exp_charges[index]; // found peak match - const double abs_err_DA = std::abs(theo_mz - exp_mz); - if (exp_z == z && abs_err_DA < max_dist_dalton) + const double abs_err_Da = std::abs(theo_mz - exp_mz); + if (exp_z == z && abs_err_Da < max_dist_dalton) { if (!peak_matched[index]) { const double intensity = exp_spectrum[index].getIntensity(); - y_mean_err += intensity * abs_err_DA; + y_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; y_ions[N-1 - i] += intensity; ++matches; @@ -861,6 +864,7 @@ class OpenNuXL : } } + #ifdef CONSIDER_AA_LOSSES // block peaks matching to AA related neutral losses so they get counted for explained peak fraction calculation // b-H2O @@ -948,7 +952,7 @@ class OpenNuXL : hyperScore = 0; MIC = 0; Morph = 0; - err = fragment_mass_tolerance_unit_ppm ? 2000.0 * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + err = fragment_mass_tolerance; } else { @@ -959,7 +963,7 @@ class OpenNuXL : for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum MIC /= TIC; Morph = b_ion_count + y_ion_count + MIC; - err = (y_mean_err + b_mean_err)/(b_sum + y_sum); + err = (y_mean_err + b_mean_err)/(b_ion_count + y_ion_count); } // match precusor ions z = 1..pc_charge @@ -1220,7 +1224,7 @@ class OpenNuXL : } #endif const double intensity = exp_spectrum[index].getIntensity(); - b_mean_err += intensity * abs_err_Da; + b_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; b_ions[i] += intensity; peak_matched[index] = true; @@ -1231,8 +1235,8 @@ class OpenNuXL : } } } - } - + } + // match y-ions for (Size z = 1; z <= max_z; ++z) { @@ -1261,7 +1265,7 @@ class OpenNuXL : const double abs_err_Da = std::abs(theo_mz - exp_mz); if (exp_z == z && abs_err_Da < max_dist_dalton) { - if (!peak_matched[index]) +// if (!peak_matched[index]) { #ifdef FILTER_AMBIGIOUS_PEAKS // skip ambigious matches @@ -1271,7 +1275,7 @@ class OpenNuXL : } #endif const double intensity = exp_spectrum[index].getIntensity(); - y_mean_err += intensity * abs_err_Da; + y_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; y_ions[N-1 - i] += intensity; peak_matched[index] = true; @@ -1374,7 +1378,7 @@ class OpenNuXL : plss_hyperScore = 0; plss_MIC = 0; plss_Morph = 0; - plss_err = fragment_mass_tolerance_unit_ppm ? 2000.0 * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; + plss_err = fragment_mass_tolerance; } else { @@ -1385,7 +1389,7 @@ class OpenNuXL : for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum plss_MIC /= TIC; plss_Morph = b_ion_count + y_ion_count + plss_MIC; - plss_err = (y_mean_err + b_mean_err)/(b_sum + y_sum); + plss_err = (y_mean_err + b_mean_err)/(b_ion_count + y_ion_count); } // match (partially) shifted precusor ions z = 1..pc_charge @@ -1519,7 +1523,7 @@ class OpenNuXL : plss_im_MIC /= TIC; // if we only have 1 peak assume some kind of average error to not underestimate the real error to much - plss_err = plss_Morph > 2 ? plss_err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; +// plss_err = plss_Morph > 2 ? plss_err : fragment_mass_tolerance; const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000; @@ -1645,8 +1649,8 @@ score += ah.mass_error_p * 1.15386068 const double ret = 1.0 * ah.total_loss_score + 0.5 * ah.partial_loss_score + 1.0 * ah.mass_error_p - - 0.1 * ah.err - - 0.1 * ah.pl_err + - 0.001 * ah.err + - 0.001 * ah.pl_err + isXL * 0.1 * ah.marker_ions_score + 1.0 * ah.total_MIC + isXL * (ah.pl_pc_MIC + ah.precursor_score) @@ -1799,9 +1803,6 @@ static void scoreXLIons_( #ifdef DEBUG_OpenNuXL LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif - // cap plss_err to something larger than the mean_mz * max_ppm_error - float ft_da = fragment_mass_tolerance_unit_ppm ? fragment_mass_tolerance * 1e-6 * 1000.0 : fragment_mass_tolerance; - if (plss_err > ft_da) plss_err = ft_da; } // De novo tagger @@ -2841,7 +2842,7 @@ static void scoreXLIons_( float partial_loss_sub_score(0), marker_ions_sub_score(0), plss_MIC(0), - plss_err(1.0), + plss_err(fragment_mass_tolerance), plss_Morph(0), plss_modds(0); @@ -4765,10 +4766,11 @@ static void scoreXLIons_( void filterPeakInterference_(PeakMap& spectra, const map& purities, double fragment_mass_tolerance = 20.0, bool fragment_mass_tolerance_unit_ppm = true) { + double filtered_peaks_count{0}; + size_t filtered_spectra{0}; for (auto& s : spectra) { unordered_set idx_to_remove; - cout << s.getNativeID() << " " << purities.size() << endl; auto it = purities.find(s.getNativeID()); if (it != purities.end()) { @@ -4785,11 +4787,14 @@ static void scoreXLIons_( for (size_t i = 0; i != s.size(); ++i) { // add indices we don't want to remove if (idx_to_remove.find(i) == idx_to_remove.end()) idx_to_keep.push_back(i); - } - cout << "Filtered out " << idx_to_remove.size() << " peaks matching to precursor inference." << endl; + } + filtered_peaks_count += idx_to_remove.size(); s.select(idx_to_keep); } + ++filtered_spectra; } + OPENMS_LOG_INFO << "Filtered out " << filtered_peaks_count << " peaks in total that matched to precursor interference." << endl; + if (filtered_spectra > 0) OPENMS_LOG_INFO << " On average " << filtered_peaks_count / (double)filtered_spectra << " peaks per MS2." << endl; } ExitCodes main_(int, const char**) override @@ -4843,7 +4848,6 @@ static void scoreXLIons_( InternalCalibration ic; // only filled if pcrecalibration is set and there are enough calibrants - // autotune (only works if non-XL peptides present) set skip_peptide_spectrum; double global_fragment_error(0); @@ -4881,7 +4885,7 @@ static void scoreXLIons_( sse.setParameters(p); cout << "Running autotune..." << endl; sse.search(in_mzml, in_db, prot_ids, pep_ids); - + /// try to run percolator { vector perc_prot_ids; @@ -5034,9 +5038,20 @@ static void scoreXLIons_( vector median_fragment_error_ppm_abs; vector median_fragment_error_ppm; vector precursor_error_ppm; + double mean_prefix_ions_fraction{}, mean_suffix_ions_fraction{}; for (const auto& pi : pep_ids) { const PeptideHit& ph = pi.getHits()[0]; + if (ph.metaValueExists(Constants::UserParam::MATCHED_PREFIX_IONS_FRACTION)) + { + mean_prefix_ions_fraction += (double)ph.getMetaValue(Constants::UserParam::MATCHED_PREFIX_IONS_FRACTION); + } + + if (ph.metaValueExists(Constants::UserParam::MATCHED_SUFFIX_IONS_FRACTION)) + { + mean_suffix_ions_fraction += (double)ph.getMetaValue(Constants::UserParam::MATCHED_SUFFIX_IONS_FRACTION); + } + if (ph.metaValueExists(Constants::UserParam::FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM)) { //cout << ph.getMetaValue("median_fragment_error_ppm") << endl; @@ -5060,6 +5075,10 @@ static void scoreXLIons_( double median_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.5]; double right_precursor_mass_tolerance = precursor_error_ppm[precursor_error_ppm.size() * 0.995]; + mean_suffix_ions_fraction /= (double) pep_ids.size(); + mean_prefix_ions_fraction /= (double) pep_ids.size(); + cout << "Mean prefix/suffix ions fractino: " << mean_prefix_ions_fraction << "/" << mean_suffix_ions_fraction << endl; + if (autotune) { fragment_mass_tolerance = new_fragment_mass_tolerance; // set new fragment mass tolerance @@ -5827,7 +5846,7 @@ static void scoreXLIons_( vector y_xl_ions(b_ions.size(), 0.0); float plss_MIC(0), - plss_err(1.0), + plss_err(fragment_mass_tolerance), plss_Morph(0), plss_modds(0), plss_pc_MIC(0), @@ -6615,6 +6634,7 @@ static void scoreXLIons_( float &plss_Morph, float &plss_modds) { + OPENMS_PRECONDITION(fragment_mass_tolerance_unit_ppm, "absolute fragment mass toleranes not implemented."); const SignedSize& exp_pc_charge = exp_spectrum.getPrecursors()[0].getCharge(); if (!marker_ions_sub_score_spectrum_z1.empty()) @@ -6652,11 +6672,11 @@ static void scoreXLIons_( pl_spec->getIntegerDataArrays()[IA_CHARGE_INDEX]); plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; plss_Morph = pl_sub_scores.score; + const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; // if we only have 1 peak assume some kind of average error to not underestimate the real error to much - plss_err = plss_Morph > 2 ? pl_sub_scores.err : 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; +// plss_err = plss_Morph > 2 ? pl_sub_scores.err_ppm : fragment_mass_tolerance; - const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; plss_modds = matchOddsScore_(pl_spec->size(), fragment_mass_tolerance_Da, exp_spectrum.size(), @@ -6666,9 +6686,6 @@ static void scoreXLIons_( #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif - // cap plss_err to something larger than the mean_mz * max_ppm_error - float ft_da = fragment_mass_tolerance_unit_ppm ? fragment_mass_tolerance * 1e-6 * 1000.0 : fragment_mass_tolerance; - if (plss_err > ft_da) plss_err = ft_da; } }; From e63c4659147fc89ef1a6ee9f7c768524425e09a2 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Thu, 17 Dec 2020 10:20:55 +0100 Subject: [PATCH 152/471] experiment - y vs b intensity odds --- src/utils/OpenNuXL.cpp | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 0e3a9c9e3f4..ef327305340 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -1350,6 +1350,7 @@ class OpenNuXL : UInt y_ion_count(0), b_ion_count(0); double b_sum(0.0); + for (Size i = 0; i != b_ions.size(); ++i) { if (b_ions[i] > 0) @@ -1371,6 +1372,16 @@ class OpenNuXL : } } + /* + peptide of size N breaks into b_i and y_{N-i} ions + or with a zero-based index: b[0] -> y[N-1], b[1] -> y[N-1-1], ... + */ + size_t y_larger_than_b{0}; + for (Size i = 0; i != b_ions.size(); ++i) + { + if (b_ions[i] < y_ions[N-1-i]) y_larger_than_b++; + } + const double& TIC = exp_spectrum.getFloatDataArrays()[0][0]; if (y_ion_count == 0 && b_ion_count == 0) @@ -1543,6 +1554,15 @@ class OpenNuXL : matches); #endif + boost::math::binomial flip(N, 0.5); + if (y_larger_than_b == 0) + { + plss_modds = 1; + } + else + { + plss_modds = boost::math::cdf(boost::math::complement(flip, y_larger_than_b - 1)); + } } /* From c7f92fe3af7548e72f40824658335b3c4ea6770c Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Sat, 26 Dec 2020 21:36:15 +0100 Subject: [PATCH 153/471] factor out into new classes, removed most of the filtering --- .../ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.h | 68 + .../OpenMS/ANALYSIS/RNPXL/RNPxlAnnotatedHit.h | 250 +++ .../OpenMS/ANALYSIS/RNPXL/RNPxlConstants.h | 57 + .../OpenMS/ANALYSIS/RNPXL/RNPxlReport.h | 32 +- .../OpenMS/ANALYSIS/RNPXL/sources.cmake | 3 + .../source/ANALYSIS/RNPXL/HyperScore.cpp | 10 +- .../ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.cpp | 741 ++++++++ .../ANALYSIS/RNPXL/RNPxlParameterParsing.cpp | 2 + .../source/ANALYSIS/RNPXL/RNPxlReport.cpp | 254 +++ .../source/ANALYSIS/RNPXL/sources.cmake | 1 + src/utils/OpenNuXL.cpp | 1561 +++-------------- 11 files changed, 1691 insertions(+), 1288 deletions(-) create mode 100644 src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.h create mode 100644 src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlAnnotatedHit.h create mode 100644 src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlConstants.h create mode 100644 src/openms/source/ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.cpp diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.h new file mode 100644 index 00000000000..f28f331dd3f --- /dev/null +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.h @@ -0,0 +1,68 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2020. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#pragma once + +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +namespace OpenMS +{ +class OPENMS_DLLAPI RNPxlAnnotateAndLocate +{ + public: + + static void annotateAndLocate_( + const PeakMap& exp, + std::vector>& annotated_hits, + const RNPxlModificationMassesResult& mm, + const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, + const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, + Size max_variable_mods_per_peptide, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const RNPxlParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts); + +}; +} // namespace OpenMS + + diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlAnnotatedHit.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlAnnotatedHit.h new file mode 100644 index 00000000000..ffb25e6f712 --- /dev/null +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlAnnotatedHit.h @@ -0,0 +1,250 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2020. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#pragma once + +#include +#include // for PeakAnnotation + + +namespace OpenMS +{ +/// Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space +/// floats need to be initialized to zero as default +class RNPxlAnnotatedHit +{ + public: + /* + Slim indices/views to lookup the actual sequence + */ + StringView sequence; + SignedSize peptide_mod_index = 0; // enumeration index of the non-NA peptide modification + Size NA_mod_index = 0; // index of the NA modification + Size NA_adduct_amb_index = 0; // store index the entry in the set of ambiguous precursor adducts (e.g, C-NH3 vs. U-H2O) + + int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment + + static constexpr const char UNKNOWN_NUCLEOTIDE = '?'; + char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE; + + /** + The main score (score) is a linear combination of (weighted) subscores + + For the fast score (ignoring all shifted peaks) we calculate: + score = 1.0 * total_loss_score + + 1.0 * total_MIC + + 0.333 * mass_error_p; + + For the all-ion score we calculate: + peptides: + score = -6.486416409280039 + + 4.059968526608637 * ah.total_MIC + + 0.5842539236790404 * ah.modds + + 0.21721652155697285 * ah.total_loss_score + + 1.9988345415208777 * ah.mass_error_p; + XLs: + score = -6.648631037190969 + + 0.4688059636415974 * ah.Morph + + 4.0386886051238 * ah.MIC + + 0.5446999629799386 * ah.modds + + 0.25318342707227187 * ah.total_loss_score + + 0.12472562244230834 * ah.partial_loss_score + + 1.2107674392113372 * ah.mass_error_p + + 2.3319284783288805 * ah.pl_MIC; + */ + float score = 0; + + /** + Normalized precursor mass error score. + Mass error is assumed normally distributed with: + - mean = 0 + - sd = sqrt(precursor_mass_tolerance) => variance = precursor tolerance + */ + float mass_error_p = 0; + + // + // Scores exclusively calculated from peaks without nucleotide shifts: + // + + /** + The total loss score is the X!Tandem HyperScore calculated from b-,y-ions + without any nucleotide shift. + */ + float total_loss_score = 0; + + /** + The matched ion current in immonium (immonium_score) and precursor ions (precursor_score) + without any nucleotide shift. + + see DOI: 10.1021/pr3007045 A Systematic Investigation into the Nature of Tryptic HCD Spectra + imY = EmpiricalFormula("C8H10NO").getMonoWeight(); // 85% + imW = EmpiricalFormula("C10H11N2").getMonoWeight(); // 84% + imF = EmpiricalFormula("C8H10N").getMonoWeight(); // 84% + imL = EmpiricalFormula("C5H12N").getMonoWeight(); // I/L 76% + imH = EmpiricalFormula("C5H8N3").getMonoWeight(); // 70% + imC = EmpiricalFormula("C2H6NS").getMonoWeight(); // CaC 61% + imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); // 2% + imP = EmpiricalFormula("C4H8N").getMonoWeight(); //? + imQ = 101.0715; // 52% + imE = 102.0555; // 37% + imM = 104.0534; // 3% + */ + float immonium_score = 0; + float precursor_score = 0; + + /** + The matched ion current (MIC), average fragment error (err), and morpheus score (Morph) are calculated + for b-,y-,a-ions without nucleotide shift. Morph is just the number of matched peaks + the fraction of MIC + */ + float MIC = 0; + float err = 0; + float Morph = 0; + + /** + The match odds (-log10) of observing this number of b-,a-, and y-ions assuming a uniform distribution of noise peaks. + */ + float modds = 0; + + // + // Scores exclusively calculated from nucleotide shifted peaks: + // + + /** + The partial loss score is the X!Tandem HyperScore calculated from b-,a-, and y-ions + with nucleotide shifts. Matches from b- and a-ions are combined, i.e. a matching a_n-ion is counted as b_n-ion. + For a precursor with charge N, all fragment ion charges up to N-1 are considered. + + Calculation of HyperScore: + yFact = logfactorial_(y_ion_count); + bFact = logfactorial_(b_ion_count); + hyperScore = log1p(dot_product) + yFact + bFact; + */ + float partial_loss_score = 0; + + /** + The matched ion current (pl_MIC) of ladder ions, average fragment error (pl_err), and morpheus score (pl_Morph) are calculated + from b-,y-,a-ions with nucleotide shift. + Morph: number of matched peaks + the fraction of MIC + */ + float pl_MIC = 0; + float pl_err = 0.0; + float pl_Morph = 0; + + /* + The match odds (-log10) of observing this number of b-,a-, and y-ions with nucleotide shifts assuming a uniform distribution of noise peaks. + */ + float pl_modds = 0; + + /* + The MIC of precursor with all nucleotide shifts. + Three variants: No additional loss, loss of water, and loss ammonia. + Charge states considered: 1..N (precursor charge) + */ + float pl_pc_MIC = 0; + + /** + The matched ion current calculated from immonium ions with nucleotide shifts. + Only singly charged immonium ions are considered. + + imY = EmpiricalFormula("C8H10NO").getMonoWeight(); + imW = EmpiricalFormula("C10H11N2").getMonoWeight(); + imF = EmpiricalFormula("C8H10N").getMonoWeight(); + imH = EmpiricalFormula("C5H8N3").getMonoWeight(); + imC = EmpiricalFormula("C2H6NS").getMonoWeight(); + imP = EmpiricalFormula("C4H8N").getMonoWeight(); + imL = EmpiricalFormula("C5H12N").getMonoWeight(); + imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); + imK2 = EmpiricalFormula("C5H10N1").getMonoWeight(); + imK3 = EmpiricalFormula("C6H13N2O").getMonoWeight(); + imQ = 101.0715; + imE = 102.0555; + imM = 104.0534; + */ + float pl_im_MIC = 0; + + // + // Scores calculated from peaks with AND without nucleotide shifts: + // + + /** + The complete TIC fraction of explained peaks (total_MIC) (excludes marker ions) + For peptides: total_MIC = MIC + im_MIC + pc_MIC (b-,a-,y-ions, immonium ions, precursor ions) + For XLs: total_MIC = MIC + im_MIC + pc_MIC + pl_MIC + pl_pc_MIC + pl_im_MIC + marker_ions_sub_score + */ + float total_MIC = 0; + + /** + The matched ion current in marker ions (marker_ions_score) is not considered in scoring. + */ + float marker_ions_score = 0; + + /** + Coverage of peptide by prefix or suffix ions (fraction) + For example: PEPTIDER + 01000100 (two of eight ions observed -> 2/8) + Shifted and non-shifted are combined to determine coverage. + */ + float ladder_score = 0; + /** + Longest sequence covered in peptide by prefix or suffix ions (fraction). + Coverage of peptide by prefix or suffix ions (fraction) + For example: PEPTIDER + 01110001 (three ions form the longest sequence -> 3/8) + Shifted and non-shifted are combined to determine coverage. + */ + float sequence_score = 0; + + float best_localization_score = 0; + String localization_scores = 0; + String best_localization; + int best_localization_position = -1; // UNKNOWN + std::vector fragment_annotations; + + size_t tag_unshifted = 0; + size_t tag_shifted = 0; + size_t tag_XLed = 0; // tag that contains the transition from unshifted to shifted + + double explained_peak_fraction = 0; + double matched_theo_fraction = 0; + double wTop50 = 0; + + size_t n_theoretical_peaks = 0; + + static bool hasBetterScore(const RNPxlAnnotatedHit& a, const RNPxlAnnotatedHit& b) + { + return a.score > b.score; + } +}; +} + diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlConstants.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlConstants.h new file mode 100644 index 00000000000..00629e1b357 --- /dev/null +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlConstants.h @@ -0,0 +1,57 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2020. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#pragma once + +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +namespace OpenMS +{ +class OPENMS_DLLAPI RNPxlConstants +{ + public: + static constexpr size_t IA_CHARGE_INDEX = 0; + static constexpr size_t IA_RANK_INDEX = 1; + static constexpr size_t IA_DENOVO_TAG_INDEX = 2; +}; +} diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlReport.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlReport.h index f4b238d5d6d..fa79ca5b379 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlReport.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlReport.h @@ -42,6 +42,9 @@ #include #include #include +#include + +#include namespace OpenMS { @@ -84,7 +87,7 @@ struct OPENMS_DLLAPI RNPxlReportRowHeader static String getString(const String& separator, const StringList& meta_values_to_export); }; -/// create report +/// create PSM report struct OPENMS_DLLAPI RNPxlReport { static std::vector annotate(const PeakMap& spectra, @@ -93,6 +96,33 @@ struct OPENMS_DLLAPI RNPxlReport double marker_ions_tolerance); }; + +/// protein report +struct OPENMS_DLLAPI RNPxlProteinReport +{ + static void annotateProteinModificationForTopHits(std::vector& prot_ids, + const std::vector& peps, + TextFile& tsv_file, + bool report_decoys = false); + + static void mapAccessionToTDProteins(ProteinIdentification& prot_id, std::map& acc2protein_targets, std::map& acc2protein_decoys) + { + std::vector& proteins = prot_id.getHits(); + for (ProteinHit& protein : proteins) + { + if (protein.getMetaValue("target_decoy").toString().hasPrefix("target")) + { + acc2protein_targets[protein.getAccession()] = &protein; + } + else + { + acc2protein_decoys[protein.getAccession()] = &protein; + } + } + } + +}; + } diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake b/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake index b42debfbb9e..574599c7ade 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake @@ -7,6 +7,9 @@ HyperScore.h ModifiedPeptideGenerator.h MorpheusScore.h PScore.h +RNPxlAnnotateAndLocate.h +RNPxlAnnotatedHit.h +RNPxlConstants.h RNPxlFragmentAdductDefinition.h RNPxlFragmentAnnotationHelper.h RNPxlFragmentIonGenerator.h diff --git a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp index 892b90f23a3..17ccb372a89 100644 --- a/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/HyperScore.cpp @@ -129,8 +129,6 @@ namespace OpenMS bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum, - std::vector& b_ions, - std::vector& y_ions, PSMDetail& d) { if (exp_spectrum.size() < 1 || theo_spectrum.size() < 1) @@ -139,12 +137,6 @@ namespace OpenMS return 0.0; } - bool store_ion_intensities = true; - if (b_ions.empty() || y_ions.empty()) - { - store_ion_intensities = false; - } - // TODO this assumes only one StringDataArray is present and it is the right one const PeakSpectrum::StringDataArray* ion_names; if (theo_spectrum.getStringDataArrays().size() > 0) @@ -170,7 +162,7 @@ namespace OpenMS const double theo_mz{(*it).getMZ()}; const double exp_int{it.ref().getIntensity()}; const double theo_int{(*it).getIntensity()}; - abs_error += Math::getPPMAbs(theo, exp_mz); + abs_error += Math::getPPMAbs(theo_mz, exp_mz); dot_product += theo_int * exp_int; /* * mass_error */; // fragment annotations in XL-MS data are more complex and do not start with the ion type, but the ion type always follows after a $ auto i = it.refIdx(); diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.cpp new file mode 100644 index 00000000000..a53b6809a8a --- /dev/null +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlAnnotateAndLocate.cpp @@ -0,0 +1,741 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2020. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#include +#include +#include +#include + +#include +#include +#include +#include +#include // for OPENMS_PRECONDITION +#include + +using namespace std; + +namespace OpenMS +{ + // static + void RNPxlAnnotateAndLocate::annotateAndLocate_( + const PeakMap& exp, + vector>& annotated_hits, + const RNPxlModificationMassesResult& mm, + const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, + const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, + Size max_variable_mods_per_peptide, + double fragment_mass_tolerance, + bool fragment_mass_tolerance_unit_ppm, + const RNPxlParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts) + { + TheoreticalSpectrumGenerator partial_loss_spectrum_generator; + auto param = partial_loss_spectrum_generator.getParameters(); + param.setValue("add_first_prefix_ion", "true"); + param.setValue("add_abundant_immonium_ions", "false"); // we add them manually for charge 1 + param.setValue("add_precursor_peaks", "true"); + param.setValue("add_all_precursor_charges", "false"); // we add them manually for every charge + param.setValue("add_metainfo", "true"); + param.setValue("add_a_ions", "true"); + param.setValue("add_b_ions", "true"); + param.setValue("add_c_ions", "false"); + param.setValue("add_x_ions", "false"); + param.setValue("add_y_ions", "true"); + param.setValue("add_z_ions", "false"); + param.setValue("add_internal_fragments", "true"); + partial_loss_spectrum_generator.setParameters(param); +#ifdef _OPENMP +#pragma omp parallel for +#endif + for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) + { + if (annotated_hits[scan_index].empty()) { continue; } + + const PeakSpectrum & exp_spectrum = exp[scan_index]; + const Size & precursor_charge = exp_spectrum.getPrecursors()[0].getCharge(); + + for (auto & a : annotated_hits[scan_index]) + { + // get unmodified string + const String unmodified_sequence = a.sequence.getString(); + + // initialize result fields + a.best_localization = unmodified_sequence; + a.best_localization_score = 0; + + AASequence aas(AASequence::fromString(unmodified_sequence)); + + // reapply modifications (because for memory reasons we only stored the index and recreation is fast) + vector all_modified_peptides; + ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications, aas); + ModifiedPeptideGenerator::applyVariableModifications(variable_modifications, aas, max_variable_mods_per_peptide, all_modified_peptides); + + // sequence with modifications - note: reannotated version requires much more memory heavy AASequence object + const AASequence& fixed_and_variable_modified_peptide = all_modified_peptides[a.peptide_mod_index]; + const double fixed_and_variable_modified_peptide_weight = fixed_and_variable_modified_peptide.getMonoWeight(); + + // determine NA on precursor from index in map + auto mod_combinations_it = mm.mod_combinations.cbegin(); + std::advance(mod_combinations_it, a.NA_mod_index); + const String precursor_na_adduct = *mod_combinations_it->second.begin(); // TODO: check if it is enough to consider only first precursor adduct ???????????????????????????????????????????????????????? + const double precursor_na_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); + + // we don't localize on non-cross-links + if (precursor_na_adduct == "none") { continue; } + + // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum + // 1. get all possible NA fragment shifts in the MS2 (based on the precursor RNA/DNA) + OPENMS_LOG_DEBUG << "Precursor NA adduct: " << precursor_na_adduct << endl; + + const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_na_adduct).feasible_adducts; + + if (feasible_MS2_adducts.empty()) { continue; } // should not be the case - check case of no nucleotide but base fragment ? + + // 2. retrieve the (nucleotide specific) fragment adducts for the cross-linked nucleotide (annotated in main search) + auto nt_to_adducts = std::find_if(feasible_MS2_adducts.begin(), feasible_MS2_adducts.end(), + [&a](NucleotideToFeasibleFragmentAdducts const & item) + { + return (item.first == a.cross_linked_nucleotide); + }); + + OPENMS_POSTCONDITION(nt_to_adducts != feasible_MS2_adducts.end(), "Nucleotide not found in mapping to feasible adducts.") + + const vector& partial_loss_modification = nt_to_adducts->second; + + // get marker ions (these are not specific to the cross-linked nucleotide but also depend on the whole oligo bound to the precursor) + const vector& marker_ions = all_feasible_adducts.at(precursor_na_adduct).marker_ions; + OPENMS_LOG_DEBUG << "Marker ions used for this Precursor NA adduct: " << endl; + for (auto & fa : marker_ions) + { + OPENMS_LOG_DEBUG << fa.name << " " << fa.mass << endl; + } + + // generate total loss spectrum for the fixed and variable modified peptide (without NAs) (using the settings for partial loss generation) + // but as we also add the abundant immonium ions for charge 1 and precursor ions for all charges to get a more complete annotation + // (these have previously not been used in the scoring of the total loss spectrum) + PeakSpectrum total_loss_spectrum; + { + TheoreticalSpectrumGenerator tmp_generator; + Param new_param(partial_loss_spectrum_generator.getParameters()); + new_param.setValue("add_all_precursor_charges", "true"); + new_param.setValue("add_abundant_immonium_ions", "true"); + new_param.setValue("add_losses", "true"); + new_param.setValue("add_term_losses", "true"); + new_param.setValue("add_a_ions", "true"); + new_param.setValue("add_internal_fragments", "true"); + tmp_generator.setParameters(new_param); + tmp_generator.getSpectrum(total_loss_spectrum, fixed_and_variable_modified_peptide, 1, precursor_charge); + } + + // add special immonium ions + RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( + unmodified_sequence, + total_loss_spectrum, + total_loss_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], + total_loss_spectrum.getStringDataArrays()[0]); + total_loss_spectrum.sortByPosition(); // need to resort after adding special immonium ions + + PeakSpectrum partial_loss_spectrum, + partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3; + + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); + partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); + RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, + fixed_and_variable_modified_peptide_weight, + precursor_na_adduct, + precursor_na_mass, + precursor_charge, + partial_loss_modification, + partial_loss_template_z1, + partial_loss_template_z2, + partial_loss_template_z3, + partial_loss_spectrum); + + // add shifted marker ions + RNPxlFragmentIonGenerator::addMS2MarkerIons( + marker_ions, + partial_loss_spectrum, + partial_loss_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], + partial_loss_spectrum.getStringDataArrays()[0]); + + partial_loss_spectrum.sortByPosition(); // need to resort after adding marker ions + + // fill annotated spectrum information + set peak_is_annotated; // experimental peak index + + // ion centric (e.g. b and y-ion) spectrum annotation that records all shifts of specific ions (e.g. y5, y5 + U, y5 + C3O) + using MapIonIndexToFragmentAnnotation = map >; + MapIonIndexToFragmentAnnotation unshifted_b_ions, unshifted_y_ions, unshifted_a_ions, shifted_b_ions, shifted_y_ions, shifted_a_ions; + vector shifted_immonium_ions, + unshifted_loss_ions, + annotated_marker_ions, + annotated_precursor_ions, + annotated_immonium_ions; + + // first annotate total loss peaks (these give no information where the actual shift occured) + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << "Annotating ion (total loss spectrum): " << fixed_and_variable_modified_peptide.toString() << endl; + #endif + vector> alignment; + + // align spectra (only allow matching charges) + DataArrays::FloatDataArray ppm_error_array; // not needed here but filled by alignment + OPXLSpectrumProcessingAlgorithms::getSpectrumAlignmentFastCharge(alignment, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + total_loss_spectrum, + exp_spectrum, + total_loss_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], + ppm_error_array); + + const PeakSpectrum::StringDataArray& total_loss_annotations = total_loss_spectrum.getStringDataArrays()[0]; + const PeakSpectrum::IntegerDataArray& total_loss_charges = total_loss_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX]; + + for (auto const & aligned : alignment) + { + // information on the experimental fragment in the alignment + const Size& fragment_index = aligned.second; + const Peak1D& fragment = exp_spectrum[fragment_index]; + const double fragment_intensity = fragment.getIntensity(); // in percent (%) + const double fragment_mz = fragment.getMZ(); + + + const String& ion_name = total_loss_annotations[aligned.first]; + const int charge = total_loss_charges[aligned.first]; + + OPENMS_PRECONDITION(exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX][fragment_index] == charge, "Charges in alignment must match."); + + // define which ion names are annotated + if (ion_name[0] == 'y') + { + Size loss_first = ion_name.find_first_of('-'); // start of loss + Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end + const bool ion_has_neutral_loss = (loss_first != string::npos); + + if (ion_has_neutral_loss) // ion with neutral loss e.g. water + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + unshifted_loss_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); + } + else // no neutral loss + { + String ion_nr_string = ion_name.substr(1, charge_pos - 1); + Size ion_number = (Size)ion_nr_string.toInt(); + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); + unshifted_y_ions[ion_number].push_back(d); + #ifdef DEBUG_OpenNuXL + const AASequence& peptide_sequence = fixed_and_variable_modified_peptide.getSuffix(ion_number); + OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; + #endif + peak_is_annotated.insert(aligned.second); + } + } + else if (ion_name[0] == 'b') + { + Size loss_first = ion_name.find_first_of('-'); // start of loss + Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end + const bool ion_has_neutral_loss = (loss_first != string::npos); + + if (ion_has_neutral_loss) + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + unshifted_loss_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); + } + else + { + String ion_nr_string = ion_name.substr(1, charge_pos - 1); + Size ion_number = (Size)ion_nr_string.toInt(); + #ifdef DEBUG_OpenNuXL + const AASequence& peptide_sequence = aas.getPrefix(ion_number); + OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; + #endif + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); + unshifted_b_ions[ion_number].push_back(d); + peak_is_annotated.insert(aligned.second); + } + } + else if (ion_name[0] == 'a') + { + Size loss_first = ion_name.find_first_of('-'); // start of loss + Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end + const bool ion_has_neutral_loss = (loss_first != string::npos); + + if (ion_has_neutral_loss) + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + unshifted_loss_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); + } + else + { + String ion_nr_string = ion_name.substr(1, charge_pos - 1); + auto ion_number = (Size)ion_nr_string.toInt(); + #ifdef DEBUG_OpenNuXL + const AASequence& peptide_sequence = aas.getPrefix(ion_number); + OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; + #endif + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); + unshifted_a_ions[ion_number].push_back(d); + peak_is_annotated.insert(aligned.second); + } + } + else if (ion_name.hasPrefix("[M+")) // precursor ion + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + annotated_precursor_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); + } + else if (ion_name.hasPrefix("i")) // immonium ion + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + annotated_immonium_ions.push_back(fa); + peak_is_annotated.insert(aligned.second); + } + else if (isupper(ion_name[0])) // internal ions + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + annotated_immonium_ions.push_back(fa); //TODO: add to annotated_internal_fragment_ions or rename vector + peak_is_annotated.insert(aligned.second); + } + } + + // generate fragment annotation strings for unshifted ions + vector fas; + if (!unshifted_b_ions.empty()) + { + const vector& fas_tmp = RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA("b", unshifted_b_ions); + fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); + } + if (!unshifted_y_ions.empty()) + { + const vector& fas_tmp = RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA("y", unshifted_y_ions); + fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); + } + if (!unshifted_a_ions.empty()) + { + const vector& fas_tmp = RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA("a", unshifted_a_ions); + fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); + } + if (!annotated_immonium_ions.empty()) + { + fas.insert(fas.end(), annotated_immonium_ions.begin(), annotated_immonium_ions.end()); + } + if (!unshifted_loss_ions.empty()) + { + fas.insert(fas.end(), unshifted_loss_ions.begin(), unshifted_loss_ions.end()); + } + + vector sites_sum_score(aas.size(), 0); + + ///////////////// + // Align partial-loss-spectrum to the experimental measured one + alignment.clear(); + ppm_error_array.clear(); + + // align spectra (only allow matching charges) + OPXLSpectrumProcessingAlgorithms::getSpectrumAlignmentFastCharge(alignment, + fragment_mass_tolerance, + fragment_mass_tolerance_unit_ppm, + partial_loss_spectrum, + exp_spectrum, + partial_loss_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], + ppm_error_array); + + #ifdef OPENUXL_DEBUG + for (size_t i = 0; i != exp_spectrum.size(); ++i) + { + OPENMS_LOG_DEBUG << "exp: " << exp_spectrum[i].getMZ() << "\t" << exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX][i] << endl; + } + #endif + + const PeakSpectrum::StringDataArray& partial_loss_annotations = partial_loss_spectrum.getStringDataArrays()[0]; + const PeakSpectrum::IntegerDataArray& partial_loss_charges = partial_loss_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX]; + + if (alignment.empty()) + { + a.fragment_annotations = fas; + continue; + } + + /* uncomment to write all annotations to a file(only makes sense if a single spectrum is searched) + MSExperiment tmp_exp; + tmp_exp.addSpectrum(total_loss_spectrum); + tmp_exp.addSpectrum(partial_loss_spectrum); + MzMLFile().store("theoretical_loss_spectrum.mzML", tmp_exp); + */ + + for (auto pair_it = alignment.begin(); pair_it != alignment.end(); ++pair_it) + { + // only annotate experimental peaks with shift - i.e. do not annotated complete loss peaks again + if (peak_is_annotated.find(pair_it->second) != peak_is_annotated.end()) { continue; } + + // information on the experimental fragment in the alignment + const Size & fragment_index = pair_it->second; + const Peak1D & fragment = exp_spectrum[fragment_index]; + const double & fragment_intensity = fragment.getIntensity(); // in percent (%) + const double & fragment_mz = fragment.getMZ(); + const int & fragment_charge = exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX][fragment_index]; + + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << "fragment_mz:" << fragment_mz << " fragment_charge:" << fragment_charge << endl; + #endif + + String ion_name = partial_loss_annotations[pair_it->first]; + const int charge = partial_loss_charges[pair_it->first]; + + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << "theo_name:" << ion_name << " theo_charge:" << charge << endl; + #endif + vector f; + + ion_name.split(' ', f); // e.g. "y3 C3O" or just "y2" + String fragment_shift_name; + if (f.size() == 2) { fragment_shift_name = f[1]; } + + String fragment_ion_name = f[0]; // e.g. y3 + + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << " intensity: " << fragment_intensity << endl; + #endif + + // define which ion names are annotated + if (fragment_ion_name.hasPrefix("y")) + { + String ion_nr_string = fragment_ion_name; + ion_nr_string.substitute("y", ""); + ion_nr_string.substitute("+", ""); // remove one or multiple '+' + auto ion_number = (Size)ion_nr_string.toInt(); + + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); + shifted_y_ions[ion_number].push_back(d); + } + else if (fragment_ion_name.hasPrefix("b")) + { + String ion_nr_string = fragment_ion_name; + ion_nr_string.substitute("b", ""); + ion_nr_string.substitute("+", ""); // remove one or multiple '+' + auto ion_number = (Size)ion_nr_string.toInt(); + + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); + shifted_b_ions[ion_number].push_back(d); + } + else if (fragment_ion_name.hasPrefix("a")) + { + String ion_nr_string = fragment_ion_name; + ion_nr_string.substitute("a", ""); + ion_nr_string.substitute("+", ""); // remove one or multiple '+' + auto ion_number = (Size)ion_nr_string.toInt(); + + RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); + shifted_a_ions[ion_number].push_back(d); + } + else if (ion_name.hasPrefix(RNPxlFragmentIonGenerator::ANNOTATIONS_MARKER_ION_PREFIX)) + { + OPENMS_LOG_DEBUG << "Marker ion aligned: " << ion_name << " fragment_mz: " << fragment_mz << " fragment_charge: " << fragment_charge << endl; + if (fragment_charge == 1) + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = 1; + fa.annotation = ion_name; + annotated_marker_ions.push_back(fa); + } + } + else if (ion_name.hasPrefix("i")) + { + if (fragment_charge == 1) + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = 1; + fa.annotation = ion_name; + shifted_immonium_ions.push_back(fa); + } + } + else if (ion_name.hasPrefix("[M+")) + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + fa.annotation = ion_name; + annotated_precursor_ions.push_back(fa); + } + else if (isupper(ion_name[0])) // shifted internal ions + { + PeptideHit::PeakAnnotation fa; + fa.mz = fragment_mz; + fa.intensity = fragment_intensity; + fa.charge = charge; + String with_plus = ion_name; + with_plus.substitute(' ', '+'); + fa.annotation = with_plus; // turn "PEPT U-H2O" into "PEPT+U-H20" + shifted_immonium_ions.push_back(fa); //TODO: add to shfited_internal_fragment_ions or rename vector + } + } + + // track shifts in n- and c-term ladders (in AAs coordinates) + // n_shifts and c_shifts will contain the summed intensities over all observed shifts at that position + // the distinction allows to easily detect prefix and suffix ladders in the next step + vector n_shifts(sites_sum_score.size(), 0); + vector c_shifts(sites_sum_score.size(), 0); + + for (Size i = 0; i != n_shifts.size(); ++i) + { + if (shifted_b_ions.find(i + 1) == shifted_b_ions.end()) { continue; } + for (auto& k : shifted_b_ions[i + 1]) { n_shifts[i] += k.intensity; } + } + + for (Size i = 0; i != n_shifts.size(); ++i) + { + if (shifted_a_ions.find(i + 1) == shifted_a_ions.end()) { continue; } + for (auto& k : shifted_a_ions[i + 1]) { n_shifts[i] += k.intensity; } + } + + for (Size i = 0; i != c_shifts.size(); ++i) + { + const Size ion_index = c_shifts.size() - i; + if (shifted_y_ions.find(ion_index) == shifted_y_ions.end()) { continue; } + for (auto& k : shifted_y_ions[ion_index]) { c_shifts[i] += k.intensity; } + } + + vector n_noshifts(sites_sum_score.size(), 0); + vector c_noshifts(sites_sum_score.size(), 0); + for (Size i = 0; i != n_noshifts.size(); ++i) + { + if (unshifted_b_ions.find(i + 1) == unshifted_b_ions.end()) { continue; } + for (auto& k : unshifted_b_ions[i + 1]) { n_noshifts[i] += k.intensity; } + } + + for (Size i = 0; i != n_noshifts.size(); ++i) + { + if (unshifted_a_ions.find(i + 1) == unshifted_a_ions.end()) { continue; } + for (auto& k : unshifted_a_ions[i + 1]) { n_noshifts[i] += k.intensity; } + } + + for (Size i = 0; i != c_noshifts.size(); ++i) + { + const Size ion_index = c_noshifts.size() - i; + if (unshifted_y_ions.find(ion_index) == unshifted_y_ions.end()) { continue; } + for (auto& k : unshifted_y_ions[ion_index]) { c_noshifts[i] += k.intensity; } + } + +#ifdef DEBUG_OpenNuXL + cout << "n:"; + for (auto& k : n_shifts) cout << k << " "; + cout << endl; + cout << "c:"; + for (auto& k : c_shifts) cout << k << " "; + cout << endl; + cout << "n0:"; + for (auto& k : n_noshifts) cout << k << " "; + cout << endl; + cout << "c0:"; + for (auto& k : c_noshifts) cout << k << " "; + cout << endl; +#endif + + // Rules implemented: + // 1. if cross-link on AA, then the prefix or suffix ending at this AA must be shifted + // 2. if the previous AA in the prefix / suffix had a stronger shifted signal, then the current on is not the correct one + // 3. if the current AA is cross-linked, then the previous AA is not cross-linked and we should observe an unshifted prefix / suffix ion + // 4. if the current AA is cross-linked, we should observe a shifted prefix / suffix ion for the next AA, too + // 5. Sum up all intensities of shifted prefix / suffix ions + for (Size i = 0; i != sites_sum_score.size(); ++i) + { + sites_sum_score[i] = 0.0; + if (n_shifts[i] == 0 && c_shifts[i] == 0) { continue; } // no shifts? no cross-link at this AA + + if (n_shifts[i] > 0) + { + if (i >= 1 && n_shifts[i - 1] > n_shifts[i]) continue; // Strong signal from shifted AA before the current one? Then skip it. + if (i >= 1 && n_noshifts[i - 1] == 0) continue; // continue if unshifted AA is missing before (left of) the shifted one. + if (i < n_shifts.size()-1 && n_shifts[i + 1] == 0) continue; // Need a shifted ladder after (maybe too conservative?) + // sum up all intensities from this position and all longer prefixes that also carry the NA + for (Size j = i; j != sites_sum_score.size(); ++j) { sites_sum_score[i] += n_shifts[j]; } + } + + if (c_shifts[i] > 0) + { + if (i < c_shifts.size()-1 && c_shifts[i + 1] > c_shifts[i]) continue; // AA after already shifted. So ignore this one. + if (i < c_noshifts.size()-1 && c_noshifts[i + 1] == 0) continue; // continue if unshifted AA is missing before (right of) the shifted one. + if (i >=1 && c_shifts[i - 1] == 0) continue; // Need a shifted ladder after (maybe too conservative?) + sites_sum_score[i] += c_shifts[i]; + // sum up all intensities from this position and all longer suffixes that also carry the NA + for (int j = i; j >= 0; --j) { sites_sum_score[i] += c_shifts[j]; } + } + } +#ifdef DEBUG_OpenNuXL + cout << "site sum score (shifted a/b/y-ions):"; + for (auto& k : sites_sum_score) cout << k << " "; + cout << endl; +#endif + + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << "Localisation based on immonium ions: "; + #endif + String aas_unmodified = aas.toUnmodifiedString(); + for (Size i = 0; i != aas_unmodified.size(); ++i) + { + String origin = String(aas_unmodified[i]); + + for (auto& a : shifted_immonium_ions) + { + // compare origin (the AA) of immonium ion to current AA + if (a.annotation[1] == aas_unmodified[i]) + { + sites_sum_score[i] += a.intensity; + } + } + } +#ifdef DEBUG_OpenNuXL + cout << "site sum score (shifted a/b/y-ions & immonium ions):"; + for (auto& k : sites_sum_score) cout << k << " "; + cout << endl; +#endif + + String best_localization = unmodified_sequence; + int best_localization_position = -1; // UNKNOWN + double best_localization_score = 0; + String localization_scores; + for (Size i = 0; i != sites_sum_score.size(); ++i) + { + if (sites_sum_score[i] > best_localization_score) { best_localization_score = sites_sum_score[i]; } + } + + for (Size i = 0; i != sites_sum_score.size(); ++i) + { + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << String::number(100.0 * sites_sum_score[i], 2); + #endif + + if (i != 0) localization_scores += ','; + if (sites_sum_score[i] > 0 ) + { + localization_scores += String::number(100.0 * sites_sum_score[i], 2); + } + else + { + localization_scores += "0"; + } + + if (best_localization_score > 0.0 && sites_sum_score[i] >= best_localization_score - 1e-6) + { + best_localization[i] = tolower(best_localization[i]); + best_localization_position = i; // Note: check if there are situations where multiple have the same score + } + } + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << endl; + #endif + + // create annotation strings for shifted fragment ions + RNPxlFragmentAnnotationHelper::addShiftedPeakFragmentAnnotation_(shifted_b_ions, + shifted_y_ions, + shifted_a_ions, + shifted_immonium_ions, + annotated_marker_ions, + annotated_precursor_ions, + fas); + + // store score of best localization(s) + a.localization_scores = localization_scores; + a.best_localization = best_localization; + a.best_localization_score = best_localization_score; + a.best_localization_position = best_localization_position; + a.fragment_annotations = fas; + + #ifdef DEBUG_OpenNuXL + OPENMS_LOG_DEBUG << "Ion centric annotation: " << endl; + OPENMS_LOG_DEBUG << "unshifted b ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("b", unshifted_b_ions) << endl; + OPENMS_LOG_DEBUG << "unshifted y ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("y", unshifted_y_ions) << endl; + OPENMS_LOG_DEBUG << "unshifted a ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("a", unshifted_a_ions) << endl; + OPENMS_LOG_DEBUG << "shifted b ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("b", shifted_b_ions) << endl; + OPENMS_LOG_DEBUG << "shifted y ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("y", shifted_y_ions) << endl; + OPENMS_LOG_DEBUG << "shifted a ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("a", shifted_a_ions) << endl; + OPENMS_LOG_DEBUG << "shifted immonium ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::shiftedIonsToString(shifted_immonium_ions) << endl; + OPENMS_LOG_DEBUG << "shifted marker ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::shiftedIonsToString(annotated_marker_ions) << endl; + OPENMS_LOG_DEBUG << "shifted precursor ions: " << endl; + OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::shiftedIonsToString(annotated_precursor_ions) << endl; + OPENMS_LOG_DEBUG << "Localization scores: "; + OPENMS_LOG_DEBUG << localization_scores << endl; + OPENMS_LOG_DEBUG << "Localisation based on ion series and immonium ions of all observed fragments: "; + OPENMS_LOG_DEBUG << best_localization << endl; + #endif + } + } + } +} // namespace + diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp index b89f4ca6a49..f8236ab9fad 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlParameterParsing.cpp @@ -343,6 +343,8 @@ RNPxlParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, ++it; // STL erase idiom (mind the pre-increment) } } + + if (fas.empty()) continue; // no feasible fragment adducts left? continue // store feasible adducts associated with a cross-link with character nucleotide[0] vector faa; diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp index 7d8a35abb56..f0fc56c3bd7 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlReport.cpp @@ -36,6 +36,8 @@ #include #include +using namespace std; + namespace OpenMS { String RNPxlReportRow::getString(const String& separator) const @@ -289,4 +291,256 @@ namespace OpenMS } return csv_rows; } + + void RNPxlProteinReport::annotateProteinModificationForTopHits(vector& prot_ids, const vector& peps, TextFile& tsv_file, bool report_decoys) + { + assert(prots.size() == 1); // support for one run only + + // protein identification run + ProteinIdentification& prot_id = prot_ids[0]; + + // create lookup accession -> protein + map acc2protein_targets; + map acc2protein_decoys; + mapAccessionToTDProteins(prot_id, acc2protein_targets, acc2protein_decoys); + + struct ModifiedRegion + { + ResidueModification* xl; + int first; + int last; + bool operator<(const ModifiedRegion& rhs) const + { + return std::tie(first, last, *xl) < std::tie(rhs.first, rhs.last, *rhs.xl); + } + }; + + // protein -> regions with XLs without AA level localization and in how many PSMs it was detected + map> modified_region_xls_targets; + map> modified_region_xls_decoys; + + map name2mod; // used to free temporary residues + + // store modification statistic for every protein + for (const PeptideIdentification& pep : peps) + { + auto& hits = pep.getHits(); + if (hits.empty()) continue; + const PeptideHit& ph = hits[0]; // only consider top hit + const std::vector& ph_evidences = ph.getPeptideEvidences(); + const int best_localization = ph.getMetaValue("NuXL:best_localization_position"); + + // create a user defined modification (at most once) + ResidueModification* xl; + const String NA = ph.getMetaValue("NuXL:NA"); + auto it = name2mod.find(NA); + if (it != name2mod.end()) + { + xl = it->second; + } + else + { + xl = new ResidueModification(); + xl->setFullId(NA); + xl->setOrigin('X'); // any AA + name2mod[NA] = xl; + } + + for (auto& ph_evidence : ph_evidences) + { + const String& acc = ph_evidence.getProteinAccession(); + const int peptide_start_in_protein = ph_evidence.getStart(); + + if (peptide_start_in_protein < 0) continue; + + const int xl_pos_in_protein = peptide_start_in_protein + best_localization; + + bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + + // not localized? annotate region + if (best_localization < 0) + { + ModifiedRegion mr; + mr.xl = xl; + mr.first = ph_evidence.getStart(); + mr.last = ph_evidence.getEnd(); + if (is_target) + { + modified_region_xls_targets[acc][mr]++; + } + else + { + modified_region_xls_decoys[acc][mr]++; + } + } + + // retrieve protein the evidence points to + ProteinHit* protein = is_target ? acc2protein_targets[acc] : acc2protein_decoys[acc]; + if (xl_pos_in_protein < protein->getSequence().size()) + { + auto mods = protein->getModifications(); // TODO: add mutable reference access + mods.AALevelSummary[xl_pos_in_protein][xl].count++; + protein->setModifications(mods); + } + } + } + + map aa2protein_count_targets; // how many proteins have that AA cross-linked + map aa2psm_count_targets; // how many PSMs have that AA cross-linked + map aa2protein_count_decoys; // how many proteins have that AA cross-linked + map aa2psm_count_decoys; // how many PSMs have that AA cross-linked + + map aa2background_freq; // AA background distribution for normalization + + for (const ProteinIdentification& prot_id : prot_ids) + { + const vector& phs = prot_id.getHits(); + for (const ProteinHit& protein : phs) + { // for all identified proteins + const String& acc = protein.getAccession(); + bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + + if (!is_target && !report_decoys) continue; // skip decoys if option is set + + const String& seq = protein.getSequence(); + + for (const char c : seq) { aa2background_freq[c] += 1.0; } + tsv_file.addLine(acc); + + auto mods = protein.getModifications(); + + // count how many PSMs support XL-ed position in the current protein + map position2psm_count; + for (const auto& p2ms : mods.AALevelSummary) + { + size_t position = p2ms.first; + for (const auto& m2s : p2ms.second) + { + const auto stat = m2s.second; + position2psm_count[position] += stat.count; + } + } + + // put string with AA, position, PSM count in sequence: e.g.: [Y123,2] + String annotated_sequence; + size_t p{0}; + + if (!position2psm_count.empty()) + { + for (const auto p2psm : position2psm_count) + { + while (p < p2psm.first) { annotated_sequence += seq[p]; ++p; } + // p now points to the modified AA + annotated_sequence += String("[") + seq[p] + String(p2psm.first + 1) + "," + String(p2psm.second) + "]"; + ++p; + } + while (p < seq.size()) { annotated_sequence += seq[p]; ++p; } // output AAs after last modification + + tsv_file.addLine(annotated_sequence); + } + else + { + tsv_file.addLine(seq); + } + + // output modification AA and count for this protein + tsv_file.addLine("Cross-link localizations:"); + set already_counted_at_protein_level; + for (const auto& p2ms : mods.AALevelSummary) + { + size_t position = p2ms.first; + + // retrieve AA a xl position + char AA_at_position = '?'; + if (seq.size() > position) + { + AA_at_position = seq[position]; + } + + // count a modified AA only once per protein for protein count + if (already_counted_at_protein_level.count(AA_at_position) == 0) + { + if (is_target) + { + aa2protein_count_targets[AA_at_position]++; + } + else + { + aa2protein_count_decoys[AA_at_position]++; + } + already_counted_at_protein_level.insert(AA_at_position); + } + + for (const auto& m2s : p2ms.second) + { + auto stat = m2s.second; + size_t count = stat.count; + if (is_target) + { + aa2psm_count_targets[AA_at_position] += count; + } + else + { + aa2psm_count_decoys[AA_at_position] += count; + } + tsv_file.addLine(m2s.first->getFullId() + ":" + AA_at_position + String(position + 1) + "(" + String(count) + ")"); + } + } + + // output list of modified regions (without AA level localization) + tsv_file.addLine("Cross-linked peptides without localization at single AA-level:"); + for (const auto& p2xlregions : modified_region_xls_targets) + { + for (const auto& region : p2xlregions.second) + { + const ModifiedRegion& r = region.first; + const size_t count = region.second; + tsv_file.addLine(r.xl->getFullId() + ":" + String(r.first + 1) + "-" + String(r.last + 1) + "(" + String(count) + ")"); + } + } + } + } + + double sum{}; + for (const auto& m : aa2background_freq) { sum += m.second; } + for (auto& m : aa2background_freq) { m.second /= sum; } + + if (report_decoys) + { + tsv_file.addLine("============================================================="); + tsv_file.addLine("Protein summary for decoy proteins:"); + tsv_file.addLine("AA:proteins"); + for (const auto& a2p : aa2protein_count_decoys) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + } + + tsv_file.addLine("============================================================="); + tsv_file.addLine("PSM summary for decoy PSMs:"); + tsv_file.addLine("AA:PSMs"); + for (const auto& a2p : aa2psm_count_decoys) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); + } + } + + tsv_file.addLine("============================================================="); + tsv_file.addLine("Protein summary for target proteins:"); + tsv_file.addLine("AA:proteins"); + for (const auto& a2p : aa2protein_count_targets) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second) + "\tfreq. normalized: " + String(a2p.second * aa2background_freq[a2p.first])); + } + + tsv_file.addLine("============================================================="); + tsv_file.addLine("PSM summary for target PSMs:"); + tsv_file.addLine("AA:PSMs"); + for (const auto& a2p : aa2psm_count_targets) + { + tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second) + "\tfreq. normalized: " + String(a2p.second * aa2background_freq[a2p.first])); + } + + for (auto m : name2mod) { delete(m.second); } // free memory + } + } diff --git a/src/openms/source/ANALYSIS/RNPXL/sources.cmake b/src/openms/source/ANALYSIS/RNPXL/sources.cmake index 1975ac87f5a..0c1a3c5c8e9 100644 --- a/src/openms/source/ANALYSIS/RNPXL/sources.cmake +++ b/src/openms/source/ANALYSIS/RNPXL/sources.cmake @@ -7,6 +7,7 @@ HyperScore.cpp ModifiedPeptideGenerator.cpp MorpheusScore.cpp PScore.cpp +RNPxlAnnotateAndLocate.cpp RNPxlFragmentAdductDefinition.cpp RNPxlFragmentAnnotationHelper.cpp RNPxlFragmentIonGenerator.cpp diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index ef327305340..98b1dc2bf57 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -58,6 +58,9 @@ #include #include #include +#include +#include +#include #include #include #include @@ -225,212 +228,6 @@ struct ImmoniumIonsInPeptide bool E = false; }; -/// Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space -/// floats need to be initialized to zero as default -class AnnotatedHit -{ - public: - /* - Slim indices/views to lookup the actual sequence - */ - StringView sequence; - SignedSize peptide_mod_index = 0; // enumeration index of the non-NA peptide modification - Size NA_mod_index = 0; // index of the NA modification - Size NA_adduct_amb_index = 0; // store index the entry in the set of ambiguous precursor adducts (e.g, C-NH3 vs. U-H2O) - - int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment - - static constexpr const char UNKNOWN_NUCLEOTIDE = '?'; - char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE; - - /** - The main score (score) is a linear combination of (weighted) subscores - - For the fast score (ignoring all shifted peaks) we calculate: - score = 1.0 * total_loss_score - + 1.0 * total_MIC - + 0.333 * mass_error_p; - - For the all-ion score we calculate: - peptides: - score = -6.486416409280039 - + 4.059968526608637 * ah.total_MIC - + 0.5842539236790404 * ah.modds - + 0.21721652155697285 * ah.total_loss_score - + 1.9988345415208777 * ah.mass_error_p; - XLs: - score = -6.648631037190969 - + 0.4688059636415974 * ah.Morph - + 4.0386886051238 * ah.MIC - + 0.5446999629799386 * ah.modds - + 0.25318342707227187 * ah.total_loss_score - + 0.12472562244230834 * ah.partial_loss_score - + 1.2107674392113372 * ah.mass_error_p - + 2.3319284783288805 * ah.pl_MIC; - */ - float score = 0; - - /** - Normalized precursor mass error score. - Mass error is assumed normally distributed with: - - mean = 0 - - sd = sqrt(precursor_mass_tolerance) => variance = precursor tolerance - */ - float mass_error_p = 0; - - // - // Scores exclusively calculated from peaks without nucleotide shifts: - // - - /** - The total loss score is the X!Tandem HyperScore calculated from b-,y-ions - without any nucleotide shift. - */ - float total_loss_score = 0; - - /** - The matched ion current in immonium (immonium_score) and precursor ions (precursor_score) - without any nucleotide shift. - - see DOI: 10.1021/pr3007045 A Systematic Investigation into the Nature of Tryptic HCD Spectra - imY = EmpiricalFormula("C8H10NO").getMonoWeight(); // 85% - imW = EmpiricalFormula("C10H11N2").getMonoWeight(); // 84% - imF = EmpiricalFormula("C8H10N").getMonoWeight(); // 84% - imL = EmpiricalFormula("C5H12N").getMonoWeight(); // I/L 76% - imH = EmpiricalFormula("C5H8N3").getMonoWeight(); // 70% - imC = EmpiricalFormula("C2H6NS").getMonoWeight(); // CaC 61% - imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); // 2% - imP = EmpiricalFormula("C4H8N").getMonoWeight(); //? - imQ = 101.0715; // 52% - imE = 102.0555; // 37% - imM = 104.0534; // 3% - */ - float immonium_score = 0; - float precursor_score = 0; - - /** - The matched ion current (MIC), average fragment error (err), and morpheus score (Morph) are calculated - for b-,y-,a-ions without nucleotide shift. Morph is just the number of matched peaks + the fraction of MIC - */ - float MIC = 0; - float err = 0; - float Morph = 0; - - /** - The match odds (-log10) of observing this number of b-,a-, and y-ions assuming a uniform distribution of noise peaks. - */ - float modds = 0; - - // - // Scores exclusively calculated from nucleotide shifted peaks: - // - - /** - The partial loss score is the X!Tandem HyperScore calculated from b-,a-, and y-ions - with nucleotide shifts. Matches from b- and a-ions are combined, i.e. a matching a_n-ion is counted as b_n-ion. - For a precursor with charge N, all fragment ion charges up to N-1 are considered. - - Calculation of HyperScore: - yFact = logfactorial_(y_ion_count); - bFact = logfactorial_(b_ion_count); - hyperScore = log1p(dot_product) + yFact + bFact; - */ - float partial_loss_score = 0; - - /** - The matched ion current (pl_MIC) of ladder ions, average fragment error (pl_err), and morpheus score (pl_Morph) are calculated - from b-,y-,a-ions with nucleotide shift. - Morph: number of matched peaks + the fraction of MIC - */ - float pl_MIC = 0; - float pl_err = 0.0; - float pl_Morph = 0; - - /* - The match odds (-log10) of observing this number of b-,a-, and y-ions with nucleotide shifts assuming a uniform distribution of noise peaks. - */ - float pl_modds = 0; - - /* - The MIC of precursor with all nucleotide shifts. - Three variants: No additional loss, loss of water, and loss ammonia. - Charge states considered: 1..N (precursor charge) - */ - float pl_pc_MIC = 0; - - /** - The matched ion current calculated from immonium ions with nucleotide shifts. - Only singly charged immonium ions are considered. - - imY = EmpiricalFormula("C8H10NO").getMonoWeight(); - imW = EmpiricalFormula("C10H11N2").getMonoWeight(); - imF = EmpiricalFormula("C8H10N").getMonoWeight(); - imH = EmpiricalFormula("C5H8N3").getMonoWeight(); - imC = EmpiricalFormula("C2H6NS").getMonoWeight(); - imP = EmpiricalFormula("C4H8N").getMonoWeight(); - imL = EmpiricalFormula("C5H12N").getMonoWeight(); - imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); - imK2 = EmpiricalFormula("C5H10N1").getMonoWeight(); - imK3 = EmpiricalFormula("C6H13N2O").getMonoWeight(); - imQ = 101.0715; - imE = 102.0555; - imM = 104.0534; - */ - float pl_im_MIC = 0; - - // - // Scores calculated from peaks with AND without nucleotide shifts: - // - - /** - The complete TIC fraction of explained peaks (total_MIC) (excludes marker ions) - For peptides: total_MIC = MIC + im_MIC + pc_MIC (b-,a-,y-ions, immonium ions, precursor ions) - For XLs: total_MIC = MIC + im_MIC + pc_MIC + pl_MIC + pl_pc_MIC + pl_im_MIC (same as above + shifted versions) - */ - float total_MIC = 0; - - /** - The matched ion current in marker ions (marker_ions_score) is not considered in scoring. - */ - float marker_ions_score = 0; - - /** - Coverage of peptide by prefix or suffix ions (fraction) - For example: PEPTIDER - 01000100 (two of eight ions observed -> 2/8) - Shifted and non-shifted are combined to determine coverage. - */ - float ladder_score = 0; - /** - Longest sequence covered in peptide by prefix or suffix ions (fraction). - Coverage of peptide by prefix or suffix ions (fraction) - For example: PEPTIDER - 01110001 (three ions form the longest sequence -> 3/8) - Shifted and non-shifted are combined to determine coverage. - */ - float sequence_score = 0; - - float best_localization_score = 0; - String localization_scores = 0; - String best_localization; - int best_localization_position = -1; // UNKNOWN - std::vector fragment_annotations; - - size_t tag_unshifted = 0; - size_t tag_shifted = 0; - size_t tag_XLed = 0; // tag that contains the transition from unshifted to shifted - - double explained_peak_fraction = 0; - double matched_theo_fraction = 0; - double wTop50 = 0; - - size_t n_theoretical_peaks = 0; - - static bool hasBetterScore(const AnnotatedHit& a, const AnnotatedHit& b) - { - return a.score > b.score; - } -}; //------------------------------------------------------------- // Doxygen docu @@ -464,9 +261,6 @@ class OpenNuXL : static constexpr double MIN_HYPERSCORE = 0.1; // hit's with lower score than this will be neglected (usually 1 or 0 matches) static constexpr double MIN_TOTAL_LOSS_IONS = 1; // minimum number of matches to unshifted ions static constexpr double MIN_SHIFTED_IONS = 1; // minimum number of matches to shifted ions (applies to XLs only) - static constexpr Size IA_CHARGE_INDEX = 0; - static constexpr Size IA_RANK_INDEX = 1; - static constexpr Size IA_DENOVO_TAG_INDEX = 2; protected: /// percolator feature set StringList feature_set_; @@ -668,6 +462,19 @@ class OpenNuXL : } */ + static double matchOddsScore_(const size_t N, const size_t matches, const double p) + { + const double pscore = boost::math::ibeta(matches + 1, N - matches, p); + if (pscore <= std::numeric_limits::min()) + { + cout.precision(17); + cout << "matches,N,p: " << matches << " " << N << " " << p << "=" << -log10(std::numeric_limits::min()) << endl; + return -log10(std::numeric_limits::min()); + } + const double minusLog10p1pscore = -log10(pscore); + return minusLog10p1pscore; + } + /* @param N number of theoretical peaks @param peak_in_spectrum number of experimental peaks @@ -775,6 +582,13 @@ class OpenNuXL : float& im_MIC, size_t& n_theoretical_peaks) { +static std::vector a_ = {0.6381814842871244,0.5757708524966219,0.3527782831613766,0.5540067995825595,0.5937077770271472,0.44059687579253287,0.5225166639570802,0.38841395620372815,0.3030517328354761,0.30979251695059956,0.30364346970241557,0.34222974087638314,0.21622567124817516,0.24461462554326147,0.25749353729143076,0.24628219274901375,0.13784446820799334,0.1495672137250644,0.2962157379587473,0.10986006002310685,0.1351953897278425,0.1278257687841041,0.30540105664584627,0.22667644652579907,0.18995271867612293,0.11525992655496903,0.22667644652579907,0.22667644652579907,0.3695782162734005,0.3695782162734005,0.5396963997850618,0.3695782162734005,0.38473739338620383,0.40192864687860225,0.41911990037100066,0.4387234158726692,0.4625932410429686,0.486463066213268,0.5103328913835674,0.5103328913835674,0.5103328913835674, +0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,}; +static std::vector b_ = {0.36098796076403716,0.4347832206269399,0.5099710884346794,0.5179672293483799,0.5631123880294966,0.5533361427988034,0.5743842109687725,0.5423494643601069,0.5760269552782373,0.5036297443627675,0.4392665770184666,0.4555728357147309,0.44068578203629283,0.4818153581717703,0.36060791092937267,0.2209935596478243,0.20127921570150337,0.11845946442071022,0.07389126171037678,0.05773828326056386,0.05017396259908622,0.04637657640949555,0.16961055844449469,0.06798833158684754,0.3170397996809263,0.3380269790757273,0.40506200961781824,0.17955033881656035,0.4337336336589538,0.5052618285906718,0.6050407460304126,0.6050407460304126,0.33802697907572726,0.47153386255306995,0.6050407460304126,0.6050407460304126,0.6050407460304126,0.6050407460304126,0.6050407460304126,0.6050407460304126,0.6050407460304126, +0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,}; +static std::vector y_ = {0.2565006415119941,0.45945372412717844,0.5115897779268463,0.5755301366035181,0.5848527137044559,0.5930609869981058,0.6076345273266521,0.6200719791091611,0.6136770720442932,0.6146578764556351,0.6279320448204195,0.6391734877807232,0.6108431180748586,0.5674428548097566,0.5129822532754515,0.6840850182019967,0.5483712842406266,0.24344021427549448,0.35994473654661996,0.4434850423849219,0.452735096428622,0.25291947015843297,0.3767693801420614,0.5301810038419658,0.21555832324685273,0.23211081378876122,0.2872560096622122,0.2872560096622122,0.3767693801420614,0.5473238809294039,0.47556492012642165,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614, +0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,}; + OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); OPENMS_PRECONDITION(total_loss_template_z1_b_ions.size() == total_loss_template_z1_y_ions.size(), "b- and y-ion arrays must have same size."); @@ -798,6 +612,8 @@ class OpenNuXL : { for (Size z = 1; z <= max_z; ++z) { + n_theoretical_peaks += total_loss_template_z1_b_ions.size(); + for (Size i = 0; i < total_loss_template_z1_b_ions.size(); ++i) { const double theo_mz = (total_loss_template_z1_b_ions[i] + diff2b @@ -816,7 +632,8 @@ class OpenNuXL : { if (!peak_matched[index]) { - const double intensity = exp_spectrum[index].getIntensity(); + double intensity = exp_spectrum[index].getIntensity(); + intensity = (diff2b == 0.0) ? intensity * b_[i] : intensity * a_[i]; ////////////////////////////////// fragment background freq scaling dot_product += intensity; if (b_ions[i] == 0) // only b-ion mass error otherwise counts don't match for mean err calculation { @@ -827,7 +644,6 @@ class OpenNuXL : peak_matched[index] = true; } } - ++n_theoretical_peaks; } } } @@ -835,6 +651,8 @@ class OpenNuXL : // match y-ions for (Size z = 1; z <= max_z; ++z) { + n_theoretical_peaks += total_loss_template_z1_y_ions.size(); + for (Size i = 0; i < total_loss_template_z1_y_ions.size(); ++i) { const double theo_mz = (total_loss_template_z1_y_ions[i] + (z-1) * Constants::PROTON_MASS_U) / z; @@ -852,7 +670,9 @@ class OpenNuXL : { if (!peak_matched[index]) { - const double intensity = exp_spectrum[index].getIntensity(); + double intensity = exp_spectrum[index].getIntensity(); + intensity = intensity * y_[i]; ////////////////////////////////// fragment background freq scaling + y_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; y_ions[N-1 - i] += intensity; @@ -860,7 +680,6 @@ class OpenNuXL : peak_matched[index] = true; } } - ++n_theoretical_peaks; } } @@ -883,10 +702,7 @@ class OpenNuXL : const double abs_err_DA = std::abs(theo_mz - exp_mz); if (exp_z == z && abs_err_DA < max_dist_dalton) { - if (!peak_matched[index]) - { - peak_matched[index] = true; - } + peak_matched[index] = true; } } } @@ -908,10 +724,7 @@ class OpenNuXL : const double abs_err_DA = std::abs(theo_mz - exp_mz); if (exp_z == z && abs_err_DA < max_dist_dalton) { - if (!peak_matched[index]) - { - peak_matched[index] = true; - } + peak_matched[index] = true; } } } @@ -942,6 +755,15 @@ class OpenNuXL : } } + /* + peptide of size N breaks into b_i and y_{N-i} ions + or with a zero-based index: b[0] -> y[N-1], b[1] -> y[N-1-1], ... + size_t y_larger_than_b{0}; + for (Size i = 0; i != b_ions.size(); ++i) + { + if (b_ions[i] < y_ions[N-1-i]) y_larger_than_b++; + } +*/ OPENMS_PRECONDITION(exp_spectrum.getFloatDataArrays()[0].getName() == "TIC", "No TIC stored in spectrum meta data."); OPENMS_PRECONDITION(exp_spectrum.getFloatDataArrays()[0].size() == 1, "Exactly one TIC expected."); @@ -1082,6 +904,7 @@ class OpenNuXL : const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000; +/* #ifdef MODDS_ON_ABY_IONS_ONLY modds = matchOddsScore_(total_loss_template_z1_b_ions.size() + total_loss_template_z1_y_ions.size(), fragment_mass_tolerance_Da, @@ -1095,6 +918,17 @@ class OpenNuXL : exp_spectrum.back().getMZ(), matches); #endif +*/ + const double p_random_match = exp_spectrum.getFloatDataArrays()[1][0]; + OPENMS_PRECONDITION(n_theoretical_peaks > 0, "Error: no theoretical peaks are generated"); + modds = matchOddsScore_(n_theoretical_peaks, matches, p_random_match); +/* + boost::math::binomial flip(N-1, 0.5); + if (y_larger_than_b > 0) + { + modds += -log10(boost::math::cdf(boost::math::complement(flip, y_larger_than_b - 1))); + } +*/ } static void scoreShiftedLadderIons_( @@ -1122,6 +956,10 @@ class OpenNuXL : size_t& n_theoretical_peaks, bool is_decoy) { + +static std::vector xl_a_ = {0.3659528914710744,0.47861728235068857,0.42071800758257055,0.5033640127522735,0.5895282639501609,0.49264930296695003,0.5324411204304591,0.48417463865923027,0.5511271154003025,0.5286803949442149,0.7173140531939944,0.336435471054921,0.4859101632376203,0.5024262214061576,0.46840208095976715,0.40809322953700483,0.3167094903810921,0.18129098288335982,0.4189105949805667,0.3330045922905184,0.3126071182614005,0.0650657360415093,0.40059551576627994,0.24183385621259657,0.17535844006882048,0.28364985698456463,0.433598827728014,0.27286545915347155,0.17535844006882048,0.24183385621259657,0.16767660150073574,0.32361968601164226,0.656809394243162,0.5729006723867871,0.4889919505304121,0.656809394243162,0.7021597756570445,0.7475101570709268,0.7928605384848093,0.7928605384848093,0.7928605384848093}; +static std::vector xl_b_ = {0.2491938528289777,0.3856151839213907,0.3647776031187359,0.5407667409164766,0.48483561551239046,0.545482943034812,0.44176624959405336,0.4892070682435069,0.5821888866263324,0.5283814756892558,0.5874975667022032,0.5254550930392076,0.6008338026815329,0.6255675366401964,0.5644205635354829,0.4547628038391301,0.3373921521612854,0.32736271323930605,0.29693905198602577,0.4331622745676728,0.2866614892568747,0.41334354567005543,0.26789101676894134,0.15648636150792897,0.03829355836488023,0.051609876958974295,0.06627620698070251,0.07546738423116832,0.11156988263191558,0.32875347958219475,0.14034341782502044,0.1891158141543777,0.28984234629777234,0.28984234629777234,0.28984234629777234,0.3524087974901858,0.3524087974901858,0.3524087974901858,0.3524087974901858,0.3524087974901858,0.3524087974901858}; +static std::vector xl_y_ = {0.2222310518617074,0.22733216758392177,0.35054745332681947,0.37174426433751473,0.41759826478801526,0.4269329894992057,0.4705619772415399,0.552562608306239,0.6461531416854231,0.5530968264015448,0.6025099662697077,0.5478810430654834,0.5571688470181058,0.5504295835175378,0.5390253808536244,0.4847596410095063,0.5018553373891388,0.473181377276754,0.5860391279941947,0.5556416220543001,0.3859448483873362,0.651387747360435,0.516376393935597,0.4093617866644474,0.4469048380712779,0.2713822504471235,0.24260619760761046,0.2337540058421485,0.319634600171193,0.35700263742531846,0.4479621597068155,0.17596775433173067,0.34805080737787986,0.3052687956612212,0.26248678394456265,0.34805080737787986,0.34805080737787986,0.34805080737787986,0.34805080737787986,0.34805080737787986,0.34805080737787986}; OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); @@ -1177,6 +1015,7 @@ class OpenNuXL : double dot_product(0.0), b_mean_err(0.0), y_mean_err(0.0); const Size N = intensity_sum.size(); // number of bonds = length of peptide - 1 + size_t n_theoretical_XL_peaks(0); size_t matches(0); // maximum charge considered @@ -1189,18 +1028,22 @@ class OpenNuXL : { for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { - + n_theoretical_XL_peaks += partial_loss_template_z1_b_ions.size(); ////////////// !!!!!!!!!!!!!!!!!!!!!!!!! skip dangerous adduct because there is a tag with same mass // TODO move out? +#ifdef FILTER_SHIFTED_PEAKS_THAT_MATCH_AA_TAGS auto it = std::find(exp_spectrum.getStringDataArrays()[0].begin(), exp_spectrum.getStringDataArrays()[0].end(), fa.name); bool has_tag_that_matches_fragmentadduct = (it != exp_spectrum.getStringDataArrays()[0].end()); +#endif for (Size i = 0; i < partial_loss_template_z1_b_ions.size(); ++i) { const double theo_mz = (partial_loss_template_z1_b_ions[i] + fa.mass + diff2b + (z-1) * Constants::PROTON_MASS_U) / z; +#ifdef FILTER_SHIFTED_PEAKS_THAT_MATCH_AA_TAGS if (has_tag_that_matches_fragmentadduct && ambigious_match(theo_mz, z, fa.name)) continue; +#endif const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; @@ -1223,7 +1066,8 @@ class OpenNuXL : if (ambigious_match(partial_loss_template_z1_b_ions[i - 1], partial_loss_template_z1_b_ions[i] + fa.mass)) continue; } #endif - const double intensity = exp_spectrum[index].getIntensity(); + double intensity = exp_spectrum[index].getIntensity(); + intensity = diff2b == 0.0 ? intensity * xl_b_[i] : intensity * xl_a_[i]; ////////////////////////////////// fragment background freq scaling b_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; b_ions[i] += intensity; @@ -1231,7 +1075,6 @@ class OpenNuXL : matches++; } } - ++n_theoretical_peaks; } } } @@ -1242,10 +1085,13 @@ class OpenNuXL : { for (const RNPxlFragmentAdductDefinition & fa : partial_loss_modification) { -////////////// !!!!!!!!!!!!!!!!!!!!!!!!! skip dangerous adduct because there is a tag with same mass + + n_theoretical_XL_peaks += partial_loss_template_z1_y_ions.size() - 1; +#ifdef FILTER_SHIFTED_PEAKS_THAT_MATCH_AA_TAGS + ////////////// !!!!!!!!!!!!!!!!!!!!!!!!! skip dangerous adduct because there is a tag with same mass auto it = std::find(exp_spectrum.getStringDataArrays()[0].begin(), exp_spectrum.getStringDataArrays()[0].end(), fa.name); bool has_tag_that_matches_fragmentadduct = (it != exp_spectrum.getStringDataArrays()[0].end()); - +#endif for (Size i = 1; i < partial_loss_template_z1_y_ions.size(); ++i) // Note that we start at (i=1 -> y2) as trypsin would otherwise not cut at cross-linking site { const double theo_mz = (partial_loss_template_z1_y_ions[i] + fa.mass @@ -1253,8 +1099,9 @@ class OpenNuXL : const double max_dist_dalton = fragment_mass_tolerance_unit_ppm ? theo_mz * fragment_mass_tolerance * 1e-6 : fragment_mass_tolerance; +#ifdef FILTER_SHIFTED_PEAKS_THAT_MATCH_AA_TAGS if (has_tag_that_matches_fragmentadduct && ambigious_match(theo_mz, z, fa.name)) continue; - +#endif // iterate over peaks in experimental spectrum in given fragment tolerance around theoretical peak Size index = exp_spectrum.findNearest(theo_mz); @@ -1265,7 +1112,7 @@ class OpenNuXL : const double abs_err_Da = std::abs(theo_mz - exp_mz); if (exp_z == z && abs_err_Da < max_dist_dalton) { -// if (!peak_matched[index]) + if (!peak_matched[index]) { #ifdef FILTER_AMBIGIOUS_PEAKS // skip ambigious matches @@ -1274,7 +1121,8 @@ class OpenNuXL : if (ambigious_match(partial_loss_template_z1_y_ions[i - 1], partial_loss_template_z1_y_ions[i] + fa.mass)) continue; } #endif - const double intensity = exp_spectrum[index].getIntensity(); + double intensity = exp_spectrum[index].getIntensity(); + intensity = intensity * xl_y_[i]; ////////////////////////////////// fragment background freq scaling y_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; y_ions[N-1 - i] += intensity; @@ -1282,7 +1130,6 @@ class OpenNuXL : matches++; } } - ++n_theoretical_peaks; } } } @@ -1375,13 +1222,12 @@ class OpenNuXL : /* peptide of size N breaks into b_i and y_{N-i} ions or with a zero-based index: b[0] -> y[N-1], b[1] -> y[N-1-1], ... - */ size_t y_larger_than_b{0}; for (Size i = 0; i != b_ions.size(); ++i) { if (b_ions[i] < y_ions[N-1-i]) y_larger_than_b++; } - +*/ const double& TIC = exp_spectrum.getFloatDataArrays()[0][0]; if (y_ion_count == 0 && b_ion_count == 0) @@ -1437,7 +1283,7 @@ class OpenNuXL : matches++; } } - ++n_theoretical_peaks; + ++n_theoretical_XL_peaks; } } } @@ -1462,7 +1308,7 @@ class OpenNuXL : matches++; } } - ++n_theoretical_peaks; + ++n_theoretical_XL_peaks; }; static const double imY = EmpiricalFormula("C8H10NO").getMonoWeight(); @@ -1536,6 +1382,7 @@ class OpenNuXL : // if we only have 1 peak assume some kind of average error to not underestimate the real error to much // plss_err = plss_Morph > 2 ? plss_err : fragment_mass_tolerance; +/* const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000; #ifdef MODDS_ON_ABY_IONS_ONLY @@ -1547,28 +1394,33 @@ class OpenNuXL : (int)plss_Morph); #else plss_modds = matchOddsScore_( - n_theoretical_peaks, + n_theoretical_XL_peaks, fragment_mass_tolerance_Da, exp_spectrum.size(), exp_spectrum.back().getMZ(), matches); #endif +*/ - boost::math::binomial flip(N, 0.5); - if (y_larger_than_b == 0) - { - plss_modds = 1; - } - else + assert(n_theoretical_XL_peaks != 0); + + const double p_random_match = exp_spectrum.getFloatDataArrays()[1][0]; + plss_modds = matchOddsScore_(n_theoretical_XL_peaks, matches, p_random_match); + n_theoretical_peaks += n_theoretical_XL_peaks; + +/* + boost::math::binomial flip(N-1, 0.5); + if (y_larger_than_b > 0) { - plss_modds = boost::math::cdf(boost::math::complement(flip, y_larger_than_b - 1)); + plss_modds += -log10(boost::math::cdf(boost::math::complement(flip, y_larger_than_b - 1))); } +*/ } /* * Combine subscores of all-ion scoring. */ - static float calculateCombinedScore(const AnnotatedHit& ah, + static float calculateCombinedScore(const RNPxlAnnotatedHit& ah, const bool isXL, const double nucleotide_mass_tags //, const double fraction_of_top50annotated @@ -1666,6 +1518,10 @@ score += ah.mass_error_p * 1.15386068 + 11.45 * ah.ladder_score + 28.09 * (ah.tag_shifted >= 1); */ + + return ah.modds + 0.00001 * ah.pl_modds; + //return sqrt(ah.pl_modds*ah.pl_modds + ah.modds*ah.modds); +/* const double ret = 1.0 * ah.total_loss_score + 0.5 * ah.partial_loss_score + 1.0 * ah.mass_error_p @@ -1678,7 +1534,7 @@ score += ah.mass_error_p * 1.15386068 + 0.1 * ah.ladder_score + 1.0 * (ah.tag_shifted >= 1); return ret; - +*/ /* * [96.45142397 49.37352197 2.61098131 -1.21298196 -4.09934265 28.64381592 @@ -1741,9 +1597,9 @@ score += ah.mass_error_p * 1.15386068 } - static float calculateFastScore(const AnnotatedHit& ah) + static float calculateFastScore(const RNPxlAnnotatedHit& ah) { - return + 1.0 * ah.total_loss_score + return ah.modds; /* + 1.0 * ah.total_MIC + 0.333 * ah.mass_error_p*/; } @@ -1787,9 +1643,9 @@ static void scoreXLIons_( auto const & r = MorpheusScore::compute(fragment_mass_tolerance * 2.0, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX]); + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX]); marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; // count marker ions @@ -1806,7 +1662,7 @@ static void scoreXLIons_( fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], intensity_sum, b_ions, y_ions, @@ -2025,7 +1881,7 @@ static void scoreXLIons_( for (size_t i = 0; i != peak_matched.size(); ++i) { if (!peak_matched[i]) { continue; } - matched_ranks.push_back(spectrum.getIntegerDataArrays()[IA_RANK_INDEX][i]); + matched_ranks.push_back(spectrum.getIntegerDataArrays()[RNPxlConstants::IA_RANK_INDEX][i]); } std::sort(matched_ranks.begin(), matched_ranks.end()); @@ -2056,7 +1912,7 @@ static void scoreXLIons_( } else { - const double rank = 1 + spectrum.getIntegerDataArrays()[IA_RANK_INDEX][i]; // ranks start at 0 -> add 1 + const double rank = 1 + spectrum.getIntegerDataArrays()[RNPxlConstants::IA_RANK_INDEX][i]; // ranks start at 0 -> add 1 r.rp += 1.0/matched * log((double)rank); top7ranks.tryAdd(rank); } @@ -2313,7 +2169,7 @@ static void scoreXLIons_( vector mzs; vector charges; for (auto const& p : spec) { mzs.push_back(p.getMZ()); } - for (auto const& p : spec.getIntegerDataArrays()[IA_CHARGE_INDEX]) { charges.push_back(p); } + for (auto const& p : spec.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX]) { charges.push_back(p); } size_t match(0); size_t in_mass_range(0); @@ -2371,13 +2227,10 @@ static void scoreXLIons_( } } - spec.getFloatDataArrays().resize(2); - - spec.getFloatDataArrays()[1].resize(1); - spec.getFloatDataArrays()[1][0] = (double)match / (double)in_mass_range; - spec.getFloatDataArrays()[1].setName("nucleotide_mass_tags"); - - + spec.getFloatDataArrays().resize(3); + spec.getFloatDataArrays()[2].resize(1); + spec.getFloatDataArrays()[2][0] = (double)match / (double)in_mass_range; + spec.getFloatDataArrays()[2].setName("nucleotide_mass_tags"); } // calculate ranks @@ -2394,10 +2247,10 @@ static void scoreXLIons_( sort(idx.begin(), idx.end(), [&spec](size_t i1, size_t i2) { return spec[i1].getIntensity() > spec[i2].getIntensity(); }); - spec.getIntegerDataArrays().resize(IA_RANK_INDEX + 1); - spec.getIntegerDataArrays()[IA_RANK_INDEX].clear(); - for (int rank : idx) { spec.getIntegerDataArrays()[IA_RANK_INDEX].push_back(rank); } - spec.getIntegerDataArrays()[IA_RANK_INDEX].setName("intensity_rank"); + spec.getIntegerDataArrays().resize(RNPxlConstants::IA_RANK_INDEX + 1); + spec.getIntegerDataArrays()[RNPxlConstants::IA_RANK_INDEX].clear(); + for (int rank : idx) { spec.getIntegerDataArrays()[RNPxlConstants::IA_RANK_INDEX].push_back(rank); } + spec.getIntegerDataArrays()[RNPxlConstants::IA_RANK_INDEX].setName("intensity_rank"); } cout << " done!" << endl; @@ -2406,15 +2259,15 @@ static void scoreXLIons_( for (auto & spec : exp) { if (spec.getMSLevel() != 2) continue; - spec.getIntegerDataArrays().resize(IA_DENOVO_TAG_INDEX + 1); - spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].resize(1); - spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = 0; + spec.getIntegerDataArrays().resize(RNPxlConstants::IA_DENOVO_TAG_INDEX + 1); + spec.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX].resize(1); + spec.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX][0] = 0; #ifdef CALCULATE_LONGEST_TAG size_t longest_tag = tagger.getLongestTagLength(spec); - spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = longest_tag; - //spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] = tagger.getLongestTag(spec).size(); // slow + spec.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX][0] = longest_tag; + //spec.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX][0] = tagger.getLongestTag(spec).size(); // slow #endif - spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX].setName("longest_tag"); + spec.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX].setName("longest_tag"); } cout << " done!" << endl; @@ -2512,6 +2365,64 @@ static void scoreXLIons_( } + // An interval has start time and end time + struct Interval_ + { + double start, end; + }; + + // Compares two intervals according to their staring time. + static bool IntervalGreater_(const Interval_& a, const Interval_& b) + { + return std::tie(b.start, b.end) < std::tie(a.start, b.end); + } + + double getAreaOfIntervalUnion_(std::vector i) + { + if (i.empty()) return 0.0; + + // sort the intervals in increasing order of start time + std::sort(i.begin(), i.end(), IntervalGreater_); + + // create an empty stack of intervals + std::stack s; + + // push the first interval to stack + s.push(i[0]); + + // Start from the next interval and merge if necessary + for (const Interval_& interval : i) + { + // get interval from stack top + Interval_ top = s.top(); + + // if current interval is not overlapping with stack top, + // push it to the stack + if (top.end < interval.start) + { + s.push(interval); + } + else if (top.end < interval.end) + { + // merge: update the end time of top + top.end = interval.end; + s.pop(); + s.push(top); + } + } + + // calculate area + double area{}; + while (!s.empty()) + { + Interval_ t = s.top(); + area += t.end - t.start; + s.pop(); + } + return area; + } + + /* @brief Filter spectra to remove noise. - Remove zero intensities @@ -2597,7 +2508,7 @@ static void scoreXLIons_( { // set Unknown charge to z=1. Otherwise we get a lot of spurious matches // to highly charged fragments in the low m/z region - DataArrays::IntegerDataArray& ia = spec.getIntegerDataArrays()[IA_CHARGE_INDEX]; // charge array + DataArrays::IntegerDataArray& ia = spec.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX]; // charge array for (int & z : ia) { if (z == 0) { z = 1; } } } #ifdef DEBUG_OpenNuXL @@ -2662,6 +2573,26 @@ static void scoreXLIons_( spec.getFloatDataArrays().resize(1); spec.getFloatDataArrays()[0].push_back(TIC); spec.getFloatDataArrays()[0].setName("TIC"); + + vector is; + const double precursor_mass = spec.getPrecursors()[0].getMZ() * spec.getPrecursors()[0].getCharge(); + for (const auto& p : spec) + { + const double mz = p.getMZ(); + if (mz > precursor_mass) break; // don't consider peaks after precursor mass + const double tol = fragment_mass_tolerance * 1e-6 * mz; + Interval_ a; + a.start = mz - tol; + a.end = mz + tol; + is.push_back(a); + } + spec.getFloatDataArrays().resize(2); + spec.getFloatDataArrays()[1].setName("P_RANDOM_MATCH"); + const double area_of_union = getAreaOfIntervalUnion_(is); + const double p_random_match = std::max(area_of_union / precursor_mass, 1e-6); // cap at low value + spec.getFloatDataArrays()[1].resize(1); + //cout << p_random_match << " " << area_of_union << " " << precursor_mass << " " << spec.getNativeID() << endl; + spec.getFloatDataArrays()[1][0] = p_random_match; } #ifdef DEBUG_OpenNuXL @@ -2677,7 +2608,7 @@ static void scoreXLIons_( if (debug_level_ > 10) MzMLFile().store("debug_filtering.mzML", exp); } - void filterTopNAnnotations_(vector>& ahs, const Size top_hits) + void filterTopNAnnotations_(vector>& ahs, const Size top_hits) { #ifdef _OPENMP #pragma omp parallel for @@ -2686,7 +2617,7 @@ static void scoreXLIons_( { // sort and keeps n best elements according to score const Size topn = top_hits > ahs[scan_index].size() ? ahs[scan_index].size() : top_hits; - std::partial_sort(ahs[scan_index].begin(), ahs[scan_index].begin() + topn, ahs[scan_index].end(), AnnotatedHit::hasBetterScore); + std::partial_sort(ahs[scan_index].begin(), ahs[scan_index].begin() + topn, ahs[scan_index].end(), RNPxlAnnotatedHit::hasBetterScore); ahs[scan_index].resize(topn); ahs[scan_index].shrink_to_fit(); } @@ -2694,7 +2625,7 @@ static void scoreXLIons_( void rescoreFastHits_( const PeakMap& exp, - vector>& annotated_hits, + vector>& annotated_hits, const RNPxlModificationMassesResult& mm, const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, @@ -2722,7 +2653,7 @@ static void scoreXLIons_( #endif for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) { - vector new_hits; + vector new_hits; // for each PSM of this spectrum for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) @@ -2747,7 +2678,7 @@ static void scoreXLIons_( // if we have a cross-link, copy PSM information for each cross-linkable nucleotides for (auto const & c : feasible_MS2_adducts) { - AnnotatedHit a(annotated_hits[scan_index][i]); + RNPxlAnnotatedHit a(annotated_hits[scan_index][i]); a.cross_linked_nucleotide = c.first; // nucleotide a.NA_adduct_amb_index = NA_adduct_amb_index; new_hits.push_back(a); @@ -2765,7 +2696,7 @@ static void scoreXLIons_( // for each PSM of this spectrum for (Size i = 0; i != annotated_hits[scan_index].size(); ++i) { - AnnotatedHit& ah = annotated_hits[scan_index][i]; + RNPxlAnnotatedHit& ah = annotated_hits[scan_index][i]; // reconstruct fixed and variable modified peptide sequence (without NA) const String& unmodified_sequence = ah.sequence.getString(); @@ -2855,7 +2786,7 @@ static void scoreXLIons_( RNPxlFragmentIonGenerator::addMS2MarkerIons( marker_ions, marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX], + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); const PeakSpectrum& exp_spectrum = exp[scan_index]; @@ -2894,7 +2825,7 @@ static void scoreXLIons_( ah.marker_ions_score = marker_ions_sub_score; ah.partial_loss_score = partial_loss_sub_score; // combined score - const double tags = exp[scan_index].getFloatDataArrays()[1][0]; + const double tags = exp[scan_index].getFloatDataArrays()[2][0]; ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); } @@ -2902,694 +2833,6 @@ static void scoreXLIons_( } } - void annotateAndLocate_( - const PeakMap& exp, - vector>& annotated_hits, - const RNPxlModificationMassesResult& mm, - const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, - const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, - Size max_variable_mods_per_peptide, - double fragment_mass_tolerance, - bool fragment_mass_tolerance_unit_ppm, - const RNPxlParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts) - { - TheoreticalSpectrumGenerator partial_loss_spectrum_generator; - auto param = partial_loss_spectrum_generator.getParameters(); - param.setValue("add_first_prefix_ion", "true"); - param.setValue("add_abundant_immonium_ions", "false"); // we add them manually for charge 1 - param.setValue("add_precursor_peaks", "true"); - param.setValue("add_all_precursor_charges", "false"); // we add them manually for every charge - param.setValue("add_metainfo", "true"); - param.setValue("add_a_ions", "true"); - param.setValue("add_b_ions", "true"); - param.setValue("add_c_ions", "false"); - param.setValue("add_x_ions", "false"); - param.setValue("add_y_ions", "true"); - param.setValue("add_z_ions", "false"); - param.setValue("add_internal_fragments", "true"); - partial_loss_spectrum_generator.setParameters(param); -#ifdef _OPENMP -#pragma omp parallel for -#endif - for (SignedSize scan_index = 0; scan_index < (SignedSize)annotated_hits.size(); ++scan_index) - { - if (annotated_hits[scan_index].empty()) { continue; } - - const PeakSpectrum & exp_spectrum = exp[scan_index]; - const Size & precursor_charge = exp_spectrum.getPrecursors()[0].getCharge(); - - for (auto & a : annotated_hits[scan_index]) - { - // get unmodified string - const String unmodified_sequence = a.sequence.getString(); - - // initialize result fields - a.best_localization = unmodified_sequence; - a.best_localization_score = 0; - - AASequence aas(AASequence::fromString(unmodified_sequence)); - - // reapply modifications (because for memory reasons we only stored the index and recreation is fast) - vector all_modified_peptides; - ModifiedPeptideGenerator::applyFixedModifications(fixed_modifications, aas); - ModifiedPeptideGenerator::applyVariableModifications(variable_modifications, aas, max_variable_mods_per_peptide, all_modified_peptides); - - // sequence with modifications - note: reannotated version requires much more memory heavy AASequence object - const AASequence& fixed_and_variable_modified_peptide = all_modified_peptides[a.peptide_mod_index]; - const double fixed_and_variable_modified_peptide_weight = fixed_and_variable_modified_peptide.getMonoWeight(); - - // determine NA on precursor from index in map - auto mod_combinations_it = mm.mod_combinations.cbegin(); - std::advance(mod_combinations_it, a.NA_mod_index); - const String precursor_na_adduct = *mod_combinations_it->second.begin(); // TODO: check if it is enough to consider only first precursor adduct ???????????????????????????????????????????????????????? - const double precursor_na_mass = EmpiricalFormula(mod_combinations_it->first).getMonoWeight(); - - // we don't localize on non-cross-links - if (precursor_na_adduct == "none") { continue; } - - // generate all partial loss spectra (excluding the complete loss spectrum) merged into one spectrum - // 1. get all possible NA fragment shifts in the MS2 (based on the precursor RNA/DNA) - OPENMS_LOG_DEBUG << "Precursor NA adduct: " << precursor_na_adduct << endl; - - const vector& feasible_MS2_adducts = all_feasible_adducts.at(precursor_na_adduct).feasible_adducts; - - if (feasible_MS2_adducts.empty()) { continue; } // should not be the case - check case of no nucleotide but base fragment ? - - // 2. retrieve the (nucleotide specific) fragment adducts for the cross-linked nucleotide (annotated in main search) - auto nt_to_adducts = std::find_if(feasible_MS2_adducts.begin(), feasible_MS2_adducts.end(), - [&a](NucleotideToFeasibleFragmentAdducts const & item) - { - return (item.first == a.cross_linked_nucleotide); - }); - - OPENMS_POSTCONDITION(nt_to_adducts != feasible_MS2_adducts.end(), "Nucleotide not found in mapping to feasible adducts.") - - const vector& partial_loss_modification = nt_to_adducts->second; - - // get marker ions (these are not specific to the cross-linked nucleotide but also depend on the whole oligo bound to the precursor) - const vector& marker_ions = all_feasible_adducts.at(precursor_na_adduct).marker_ions; - OPENMS_LOG_DEBUG << "Marker ions used for this Precursor NA adduct: " << endl; - for (auto & fa : marker_ions) - { - OPENMS_LOG_DEBUG << fa.name << " " << fa.mass << endl; - } - - // generate total loss spectrum for the fixed and variable modified peptide (without NAs) (using the settings for partial loss generation) - // but as we also add the abundant immonium ions for charge 1 and precursor ions for all charges to get a more complete annotation - // (these have previously not been used in the scoring of the total loss spectrum) - PeakSpectrum total_loss_spectrum; - { - TheoreticalSpectrumGenerator tmp_generator; - Param new_param(partial_loss_spectrum_generator.getParameters()); - new_param.setValue("add_all_precursor_charges", "true"); - new_param.setValue("add_abundant_immonium_ions", "true"); - new_param.setValue("add_losses", "true"); - new_param.setValue("add_term_losses", "true"); - new_param.setValue("add_a_ions", "true"); - new_param.setValue("add_internal_fragments", "true"); - tmp_generator.setParameters(new_param); - tmp_generator.getSpectrum(total_loss_spectrum, fixed_and_variable_modified_peptide, 1, precursor_charge); - } - - // add special immonium ions - RNPxlFragmentIonGenerator::addSpecialLysImmonumIons( - unmodified_sequence, - total_loss_spectrum, - total_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], - total_loss_spectrum.getStringDataArrays()[0]); - total_loss_spectrum.sortByPosition(); // need to resort after adding special immonium ions - - PeakSpectrum partial_loss_spectrum, - partial_loss_template_z1, - partial_loss_template_z2, - partial_loss_template_z3; - - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); - partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); - RNPxlFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, - fixed_and_variable_modified_peptide_weight, - precursor_na_adduct, - precursor_na_mass, - precursor_charge, - partial_loss_modification, - partial_loss_template_z1, - partial_loss_template_z2, - partial_loss_template_z3, - partial_loss_spectrum); - - // add shifted marker ions - RNPxlFragmentIonGenerator::addMS2MarkerIons( - marker_ions, - partial_loss_spectrum, - partial_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], - partial_loss_spectrum.getStringDataArrays()[0]); - - partial_loss_spectrum.sortByPosition(); // need to resort after adding marker ions - - // fill annotated spectrum information - set peak_is_annotated; // experimental peak index - - // ion centric (e.g. b and y-ion) spectrum annotation that records all shifts of specific ions (e.g. y5, y5 + U, y5 + C3O) - using MapIonIndexToFragmentAnnotation = map >; - MapIonIndexToFragmentAnnotation unshifted_b_ions, unshifted_y_ions, unshifted_a_ions, shifted_b_ions, shifted_y_ions, shifted_a_ions; - vector shifted_immonium_ions, - unshifted_loss_ions, - annotated_marker_ions, - annotated_precursor_ions, - annotated_immonium_ions; - - // first annotate total loss peaks (these give no information where the actual shift occured) - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << "Annotating ion (total loss spectrum): " << fixed_and_variable_modified_peptide.toString() << endl; - #endif - vector> alignment; - - // align spectra (only allow matching charges) - DataArrays::FloatDataArray ppm_error_array; // not needed here but filled by alignment - OPXLSpectrumProcessingAlgorithms::getSpectrumAlignmentFastCharge(alignment, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - total_loss_spectrum, - exp_spectrum, - total_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], - ppm_error_array); - - const PeakSpectrum::StringDataArray& total_loss_annotations = total_loss_spectrum.getStringDataArrays()[0]; - const PeakSpectrum::IntegerDataArray& total_loss_charges = total_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX]; - - for (auto const & aligned : alignment) - { - // information on the experimental fragment in the alignment - const Size& fragment_index = aligned.second; - const Peak1D& fragment = exp_spectrum[fragment_index]; - const double fragment_intensity = fragment.getIntensity(); // in percent (%) - const double fragment_mz = fragment.getMZ(); - - - const String& ion_name = total_loss_annotations[aligned.first]; - const int charge = total_loss_charges[aligned.first]; - - OPENMS_PRECONDITION(exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX][fragment_index] == charge, "Charges in alignment must match."); - - // define which ion names are annotated - if (ion_name[0] == 'y') - { - Size loss_first = ion_name.find_first_of('-'); // start of loss - Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end - const bool ion_has_neutral_loss = (loss_first != string::npos); - - if (ion_has_neutral_loss) // ion with neutral loss e.g. water - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - unshifted_loss_ions.push_back(fa); - peak_is_annotated.insert(aligned.second); - } - else // no neutral loss - { - String ion_nr_string = ion_name.substr(1, charge_pos - 1); - Size ion_number = (Size)ion_nr_string.toInt(); - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); - unshifted_y_ions[ion_number].push_back(d); - #ifdef DEBUG_OpenNuXL - const AASequence& peptide_sequence = fixed_and_variable_modified_peptide.getSuffix(ion_number); - OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; - #endif - peak_is_annotated.insert(aligned.second); - } - } - else if (ion_name[0] == 'b') - { - Size loss_first = ion_name.find_first_of('-'); // start of loss - Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end - const bool ion_has_neutral_loss = (loss_first != string::npos); - - if (ion_has_neutral_loss) - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - unshifted_loss_ions.push_back(fa); - peak_is_annotated.insert(aligned.second); - } - else - { - String ion_nr_string = ion_name.substr(1, charge_pos - 1); - Size ion_number = (Size)ion_nr_string.toInt(); - #ifdef DEBUG_OpenNuXL - const AASequence& peptide_sequence = aas.getPrefix(ion_number); - OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; - #endif - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); - unshifted_b_ions[ion_number].push_back(d); - peak_is_annotated.insert(aligned.second); - } - } - else if (ion_name[0] == 'a') - { - Size loss_first = ion_name.find_first_of('-'); // start of loss - Size charge_pos = ion_name.find_first_of('+'); // charge indicator at end - const bool ion_has_neutral_loss = (loss_first != string::npos); - - if (ion_has_neutral_loss) - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - unshifted_loss_ions.push_back(fa); - peak_is_annotated.insert(aligned.second); - } - else - { - String ion_nr_string = ion_name.substr(1, charge_pos - 1); - auto ion_number = (Size)ion_nr_string.toInt(); - #ifdef DEBUG_OpenNuXL - const AASequence& peptide_sequence = aas.getPrefix(ion_number); - OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << peptide_sequence.toString() << " intensity: " << fragment_intensity << endl; - #endif - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d("", charge, fragment_mz, fragment_intensity); - unshifted_a_ions[ion_number].push_back(d); - peak_is_annotated.insert(aligned.second); - } - } - else if (ion_name.hasPrefix("[M+")) // precursor ion - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - annotated_precursor_ions.push_back(fa); - peak_is_annotated.insert(aligned.second); - } - else if (ion_name.hasPrefix("i")) // immonium ion - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - annotated_immonium_ions.push_back(fa); - peak_is_annotated.insert(aligned.second); - } - else if (isupper(ion_name[0])) // internal ions - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - annotated_immonium_ions.push_back(fa); //TODO: add to annotated_internal_fragment_ions or rename vector - peak_is_annotated.insert(aligned.second); - } - } - - // generate fragment annotation strings for unshifted ions - vector fas; - if (!unshifted_b_ions.empty()) - { - const vector& fas_tmp = RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA("b", unshifted_b_ions); - fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); - } - if (!unshifted_y_ions.empty()) - { - const vector& fas_tmp = RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA("y", unshifted_y_ions); - fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); - } - if (!unshifted_a_ions.empty()) - { - const vector& fas_tmp = RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA("a", unshifted_a_ions); - fas.insert(fas.end(), fas_tmp.begin(), fas_tmp.end()); - } - if (!annotated_immonium_ions.empty()) - { - fas.insert(fas.end(), annotated_immonium_ions.begin(), annotated_immonium_ions.end()); - } - if (!unshifted_loss_ions.empty()) - { - fas.insert(fas.end(), unshifted_loss_ions.begin(), unshifted_loss_ions.end()); - } - - vector sites_sum_score(aas.size(), 0); - - ///////////////// - // Align partial-loss-spectrum to the experimental measured one - alignment.clear(); - ppm_error_array.clear(); - - // align spectra (only allow matching charges) - OPXLSpectrumProcessingAlgorithms::getSpectrumAlignmentFastCharge(alignment, - fragment_mass_tolerance, - fragment_mass_tolerance_unit_ppm, - partial_loss_spectrum, - exp_spectrum, - partial_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], - ppm_error_array); - - #ifdef OPENUXL_DEBUG - for (size_t i = 0; i != exp_spectrum.size(); ++i) - { - OPENMS_LOG_DEBUG << "exp: " << exp_spectrum[i].getMZ() << "\t" << exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX][i] << endl; - } - #endif - - const PeakSpectrum::StringDataArray& partial_loss_annotations = partial_loss_spectrum.getStringDataArrays()[0]; - const PeakSpectrum::IntegerDataArray& partial_loss_charges = partial_loss_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX]; - - if (alignment.empty()) - { - a.fragment_annotations = fas; - continue; - } - - /* uncomment to write all annotations to a file(only makes sense if a single spectrum is searched) - MSExperiment tmp_exp; - tmp_exp.addSpectrum(total_loss_spectrum); - tmp_exp.addSpectrum(partial_loss_spectrum); - MzMLFile().store("theoretical_loss_spectrum.mzML", tmp_exp); - */ - - for (auto pair_it = alignment.begin(); pair_it != alignment.end(); ++pair_it) - { - // only annotate experimental peaks with shift - i.e. do not annotated complete loss peaks again - if (peak_is_annotated.find(pair_it->second) != peak_is_annotated.end()) { continue; } - - // information on the experimental fragment in the alignment - const Size & fragment_index = pair_it->second; - const Peak1D & fragment = exp_spectrum[fragment_index]; - const double & fragment_intensity = fragment.getIntensity(); // in percent (%) - const double & fragment_mz = fragment.getMZ(); - const int & fragment_charge = exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX][fragment_index]; - - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << "fragment_mz:" << fragment_mz << " fragment_charge:" << fragment_charge << endl; - #endif - - String ion_name = partial_loss_annotations[pair_it->first]; - const int charge = partial_loss_charges[pair_it->first]; - - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << "theo_name:" << ion_name << " theo_charge:" << charge << endl; - #endif - vector f; - - ion_name.split(' ', f); // e.g. "y3 C3O" or just "y2" - String fragment_shift_name; - if (f.size() == 2) { fragment_shift_name = f[1]; } - - String fragment_ion_name = f[0]; // e.g. y3 - - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << "Annotating ion: " << ion_name << " at position: " << fragment_mz << " " << " intensity: " << fragment_intensity << endl; - #endif - - // define which ion names are annotated - if (fragment_ion_name.hasPrefix("y")) - { - String ion_nr_string = fragment_ion_name; - ion_nr_string.substitute("y", ""); - ion_nr_string.substitute("+", ""); // remove one or multiple '+' - auto ion_number = (Size)ion_nr_string.toInt(); - - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); - shifted_y_ions[ion_number].push_back(d); - } - else if (fragment_ion_name.hasPrefix("b")) - { - String ion_nr_string = fragment_ion_name; - ion_nr_string.substitute("b", ""); - ion_nr_string.substitute("+", ""); // remove one or multiple '+' - auto ion_number = (Size)ion_nr_string.toInt(); - - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); - shifted_b_ions[ion_number].push_back(d); - } - else if (fragment_ion_name.hasPrefix("a")) - { - String ion_nr_string = fragment_ion_name; - ion_nr_string.substitute("a", ""); - ion_nr_string.substitute("+", ""); // remove one or multiple '+' - auto ion_number = (Size)ion_nr_string.toInt(); - - RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ d(fragment_shift_name, charge, fragment_mz, fragment_intensity); - shifted_a_ions[ion_number].push_back(d); - } - else if (ion_name.hasPrefix(RNPxlFragmentIonGenerator::ANNOTATIONS_MARKER_ION_PREFIX)) - { - OPENMS_LOG_DEBUG << "Marker ion aligned: " << ion_name << " fragment_mz: " << fragment_mz << " fragment_charge: " << fragment_charge << endl; - if (fragment_charge == 1) - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = 1; - fa.annotation = ion_name; - annotated_marker_ions.push_back(fa); - } - } - else if (ion_name.hasPrefix("i")) - { - if (fragment_charge == 1) - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = 1; - fa.annotation = ion_name; - shifted_immonium_ions.push_back(fa); - } - } - else if (ion_name.hasPrefix("[M+")) - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - fa.annotation = ion_name; - annotated_precursor_ions.push_back(fa); - } - else if (isupper(ion_name[0])) // shifted internal ions - { - PeptideHit::PeakAnnotation fa; - fa.mz = fragment_mz; - fa.intensity = fragment_intensity; - fa.charge = charge; - String with_plus = ion_name; - with_plus.substitute(' ', '+'); - fa.annotation = with_plus; // turn "PEPT U-H2O" into "PEPT+U-H20" - shifted_immonium_ions.push_back(fa); //TODO: add to shfited_internal_fragment_ions or rename vector - } - } - - // track shifts in n- and c-term ladders (in AAs coordinates) - // n_shifts and c_shifts will contain the summed intensities over all observed shifts at that position - // the distinction allows to easily detect prefix and suffix ladders in the next step - vector n_shifts(sites_sum_score.size(), 0); - vector c_shifts(sites_sum_score.size(), 0); - - for (Size i = 0; i != n_shifts.size(); ++i) - { - if (shifted_b_ions.find(i + 1) == shifted_b_ions.end()) { continue; } - for (auto& k : shifted_b_ions[i + 1]) { n_shifts[i] += k.intensity; } - } - - for (Size i = 0; i != n_shifts.size(); ++i) - { - if (shifted_a_ions.find(i + 1) == shifted_a_ions.end()) { continue; } - for (auto& k : shifted_a_ions[i + 1]) { n_shifts[i] += k.intensity; } - } - - for (Size i = 0; i != c_shifts.size(); ++i) - { - const Size ion_index = c_shifts.size() - i; - if (shifted_y_ions.find(ion_index) == shifted_y_ions.end()) { continue; } - for (auto& k : shifted_y_ions[ion_index]) { c_shifts[i] += k.intensity; } - } - - vector n_noshifts(sites_sum_score.size(), 0); - vector c_noshifts(sites_sum_score.size(), 0); - for (Size i = 0; i != n_noshifts.size(); ++i) - { - if (unshifted_b_ions.find(i + 1) == unshifted_b_ions.end()) { continue; } - for (auto& k : unshifted_b_ions[i + 1]) { n_noshifts[i] += k.intensity; } - } - - for (Size i = 0; i != n_noshifts.size(); ++i) - { - if (unshifted_a_ions.find(i + 1) == unshifted_a_ions.end()) { continue; } - for (auto& k : unshifted_a_ions[i + 1]) { n_noshifts[i] += k.intensity; } - } - - for (Size i = 0; i != c_noshifts.size(); ++i) - { - const Size ion_index = c_noshifts.size() - i; - if (unshifted_y_ions.find(ion_index) == unshifted_y_ions.end()) { continue; } - for (auto& k : unshifted_y_ions[ion_index]) { c_noshifts[i] += k.intensity; } - } - -#ifdef DEBUG_OpenNuXL - cout << "n:"; - for (auto& k : n_shifts) cout << k << " "; - cout << endl; - cout << "c:"; - for (auto& k : c_shifts) cout << k << " "; - cout << endl; - cout << "n0:"; - for (auto& k : n_noshifts) cout << k << " "; - cout << endl; - cout << "c0:"; - for (auto& k : c_noshifts) cout << k << " "; - cout << endl; -#endif - - // Rules implemented: - // 1. if cross-link on AA, then the prefix or suffix ending at this AA must be shifted - // 2. if the previous AA in the prefix / suffix had a stronger shifted signal, then the current on is not the correct one - // 3. if the current AA is cross-linked, then the previous AA is not cross-linked and we should observe an unshifted prefix / suffix ion - // 4. if the current AA is cross-linked, we should observe a shifted prefix / suffix ion for the next AA, too - // 5. Sum up all intensities of shifted prefix / suffix ions - for (Size i = 0; i != sites_sum_score.size(); ++i) - { - sites_sum_score[i] = 0.0; - if (n_shifts[i] == 0 && c_shifts[i] == 0) { continue; } // no shifts? no cross-link at this AA - - if (n_shifts[i] > 0) - { - if (i >= 1 && n_shifts[i - 1] > n_shifts[i]) continue; // Strong signal from shifted AA before the current one? Then skip it. - if (i >= 1 && n_noshifts[i - 1] == 0) continue; // continue if unshifted AA is missing before (left of) the shifted one. - if (i < n_shifts.size()-1 && n_shifts[i + 1] == 0) continue; // Need a shifted ladder after (maybe too conservative?) - // sum up all intensities from this position and all longer prefixes that also carry the NA - for (Size j = i; j != sites_sum_score.size(); ++j) { sites_sum_score[i] += n_shifts[j]; } - } - - if (c_shifts[i] > 0) - { - if (i < c_shifts.size()-1 && c_shifts[i + 1] > c_shifts[i]) continue; // AA after already shifted. So ignore this one. - if (i < c_noshifts.size()-1 && c_noshifts[i + 1] == 0) continue; // continue if unshifted AA is missing before (right of) the shifted one. - if (i >=1 && c_shifts[i - 1] == 0) continue; // Need a shifted ladder after (maybe too conservative?) - sites_sum_score[i] += c_shifts[i]; - // sum up all intensities from this position and all longer suffixes that also carry the NA - for (int j = i; j >= 0; --j) { sites_sum_score[i] += c_shifts[j]; } - } - } -#ifdef DEBUG_OpenNuXL - cout << "site sum score (shifted a/b/y-ions):"; - for (auto& k : sites_sum_score) cout << k << " "; - cout << endl; -#endif - - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << "Localisation based on immonium ions: "; - #endif - String aas_unmodified = aas.toUnmodifiedString(); - for (Size i = 0; i != aas_unmodified.size(); ++i) - { - String origin = String(aas_unmodified[i]); - - for (auto& a : shifted_immonium_ions) - { - // compare origin (the AA) of immonium ion to current AA - if (a.annotation[1] == aas_unmodified[i]) - { - sites_sum_score[i] += a.intensity; - } - } - } -#ifdef DEBUG_OpenNuXL - cout << "site sum score (shifted a/b/y-ions & immonium ions):"; - for (auto& k : sites_sum_score) cout << k << " "; - cout << endl; -#endif - - String best_localization = unmodified_sequence; - int best_localization_position = -1; // UNKNOWN - double best_localization_score = 0; - String localization_scores; - for (Size i = 0; i != sites_sum_score.size(); ++i) - { - if (sites_sum_score[i] > best_localization_score) { best_localization_score = sites_sum_score[i]; } - } - - for (Size i = 0; i != sites_sum_score.size(); ++i) - { - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << String::number(100.0 * sites_sum_score[i], 2); - #endif - - if (i != 0) localization_scores += ','; - if (sites_sum_score[i] > 0 ) - { - localization_scores += String::number(100.0 * sites_sum_score[i], 2); - } - else - { - localization_scores += "0"; - } - - if (best_localization_score > 0.0 && sites_sum_score[i] >= best_localization_score - 1e-6) - { - best_localization[i] = tolower(best_localization[i]); - best_localization_position = i; // Note: check if there are situations where multiple have the same score - } - } - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << endl; - #endif - - // create annotation strings for shifted fragment ions - RNPxlFragmentAnnotationHelper::addShiftedPeakFragmentAnnotation_(shifted_b_ions, - shifted_y_ions, - shifted_a_ions, - shifted_immonium_ions, - annotated_marker_ions, - annotated_precursor_ions, - fas); - - // store score of best localization(s) - a.localization_scores = localization_scores; - a.best_localization = best_localization; - a.best_localization_score = best_localization_score; - a.best_localization_position = best_localization_position; - a.fragment_annotations = fas; - - #ifdef DEBUG_OpenNuXL - OPENMS_LOG_DEBUG << "Ion centric annotation: " << endl; - OPENMS_LOG_DEBUG << "unshifted b ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("b", unshifted_b_ions) << endl; - OPENMS_LOG_DEBUG << "unshifted y ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("y", unshifted_y_ions) << endl; - OPENMS_LOG_DEBUG << "unshifted a ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("a", unshifted_a_ions) << endl; - OPENMS_LOG_DEBUG << "shifted b ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("b", shifted_b_ions) << endl; - OPENMS_LOG_DEBUG << "shifted y ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("y", shifted_y_ions) << endl; - OPENMS_LOG_DEBUG << "shifted a ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToString("a", shifted_a_ions) << endl; - OPENMS_LOG_DEBUG << "shifted immonium ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::shiftedIonsToString(shifted_immonium_ions) << endl; - OPENMS_LOG_DEBUG << "shifted marker ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::shiftedIonsToString(annotated_marker_ions) << endl; - OPENMS_LOG_DEBUG << "shifted precursor ions: " << endl; - OPENMS_LOG_DEBUG << RNPxlFragmentAnnotationHelper::shiftedIonsToString(annotated_precursor_ions) << endl; - OPENMS_LOG_DEBUG << "Localization scores: "; - OPENMS_LOG_DEBUG << localization_scores << endl; - OPENMS_LOG_DEBUG << "Localisation based on ion series and immonium ions of all observed fragments: "; - OPENMS_LOG_DEBUG << best_localization << endl; - #endif - } - } - } /* @brief Localization step of the cross-link identification engine. 1. Generates all fragment adducts based on the attached precursor adduct @@ -3597,8 +2840,8 @@ static void scoreXLIons_( 3. Add additional meta information for PSM. */ void postScoreHits_(const PeakMap& exp, - vector >& annotated_XL_hits, - vector >& annotated_peptide_hits, + vector >& annotated_XL_hits, + vector >& annotated_peptide_hits, const RNPxlModificationMassesResult& mm, const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType& variable_modifications, @@ -3620,12 +2863,12 @@ static void scoreXLIons_( rescoreFastHits_(exp, annotated_peptide_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); } - annotateAndLocate_(exp, annotated_XL_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); - annotateAndLocate_(exp, annotated_peptide_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); + RNPxlAnnotateAndLocate::annotateAndLocate_(exp, annotated_XL_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); + RNPxlAnnotateAndLocate::annotateAndLocate_(exp, annotated_peptide_hits, mm, fixed_modifications, variable_modifications, max_variable_mods_per_peptide, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, all_feasible_adducts); } void fillSpectrumID_( - const vector& ahs, + const vector& ahs, PeptideIdentification& pi, const RNPxlModificationMassesResult& mm, const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications, @@ -3791,8 +3034,8 @@ static void scoreXLIons_( ph.setMetaValue("precursor_purity", purities.at(spec.getNativeID()).signal_proportion); } - ph.setMetaValue("nucleotide_mass_tags", (double)spec.getFloatDataArrays()[1][0]); - int maxtag = spec.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0]; + ph.setMetaValue("nucleotide_mass_tags", (double)spec.getFloatDataArrays()[2][0]); + int maxtag = spec.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX][0]; ph.setMetaValue("NuXL:aminoacid_max_tag", maxtag); const double id2maxtag = maxtag == 0 ? 0 : (ah.ladder_score * s.size()) / (double)maxtag; ph.setMetaValue("NuXL:aminoacid_id_to_max_tag_ratio", id2maxtag); @@ -3826,8 +3069,8 @@ static void scoreXLIons_( 2. Add additional meta information for PSM. */ void postProcessHits_(const PeakMap& exp, - vector >& annotated_XL_hits, - vector >& annotated_peptide_hits, + vector >& annotated_XL_hits, + vector >& annotated_peptide_hits, vector& protein_ids, vector& peptide_ids, const RNPxlModificationMassesResult& mm, @@ -3843,8 +3086,8 @@ static void scoreXLIons_( for (SignedSize scan_index = 0; scan_index < hit_count; ++scan_index) { const MSSpectrum& spec = exp[scan_index]; - vector& ahs_XL = annotated_XL_hits[scan_index]; - vector& ahs_peptide = annotated_peptide_hits[scan_index]; + vector& ahs_XL = annotated_XL_hits[scan_index]; + vector& ahs_peptide = annotated_peptide_hits[scan_index]; if (ahs_XL.empty() && ahs_peptide.empty()) continue; @@ -4012,7 +3255,7 @@ static void scoreXLIons_( const boost::math::normal & gaussian_mass_error, const double & fragment_mass_tolerance, const bool & fragment_mass_tolerance_unit_ppm, - vector & annotated_hits, + vector & annotated_hits, #ifdef _OPENMP omp_lock_t & annotated_hits_lock, #endif @@ -4037,7 +3280,7 @@ static void scoreXLIons_( scorePeptideIons_( exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], total_loss_template_z1_b_ions, total_loss_template_z1_y_ions, current_peptide_mass_without_NA, @@ -4068,7 +3311,7 @@ static void scoreXLIons_( const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); // add peptide hit - AnnotatedHit ah; + RNPxlAnnotatedHit ah; ah.mass_error_p = mass_error_score; ah.sequence = sequence; // copy StringView @@ -4111,7 +3354,7 @@ static void scoreXLIons_( // prevent vector from growing indefinitly (memory) but don't shrink the vector every time if (annotated_hits.size() >= 2 * report_top_hits) { - std::partial_sort(annotated_hits.begin(), annotated_hits.begin() + report_top_hits, annotated_hits.end(), AnnotatedHit::hasBetterScore); + std::partial_sort(annotated_hits.begin(), annotated_hits.begin() + report_top_hits, annotated_hits.end(), RNPxlAnnotatedHit::hasBetterScore); annotated_hits.resize(report_top_hits); } } @@ -4517,273 +3760,6 @@ static void scoreXLIons_( } - void mapAccessionToTDProteins(ProteinIdentification& prot_id, map& acc2protein_targets, map& acc2protein_decoys) - { - vector& proteins = prot_id.getHits(); - for (ProteinHit& protein : proteins) - { - if (protein.getMetaValue("target_decoy").toString().hasPrefix("target")) - { - acc2protein_targets[protein.getAccession()] = &protein; - } - else - { - acc2protein_decoys[protein.getAccession()] = &protein; - } - } - } - - void annotateProteinModificationForTopHits_(vector& prot_ids, const vector& peps, TextFile& tsv_file, bool report_decoys = false) - { - assert(prots.size() == 1); // support for one run only - - // protein identification run - ProteinIdentification& prot_id = prot_ids[0]; - - // create lookup accession -> protein - map acc2protein_targets; - map acc2protein_decoys; - mapAccessionToTDProteins(prot_id, acc2protein_targets, acc2protein_decoys); - - struct ModifiedRegion - { - ResidueModification* xl; - int first; - int last; - bool operator<(const ModifiedRegion& rhs) const - { - return std::tie(first, last, *xl) < std::tie(rhs.first, rhs.last, *rhs.xl); - } - }; - - // protein -> regions with XLs without AA level localization and in how many PSMs it was detected - map> modified_region_xls_targets; - map> modified_region_xls_decoys; - - map name2mod; // used to free temporary residues - - // store modification statistic for every protein - for (const PeptideIdentification& pep : peps) - { - auto& hits = pep.getHits(); - if (hits.empty()) continue; - const PeptideHit& ph = hits[0]; // only consider top hit - const std::vector& ph_evidences = ph.getPeptideEvidences(); - const int best_localization = ph.getMetaValue("NuXL:best_localization_position"); - - // create a user defined modification (at most once) - ResidueModification* xl; - const String NA = ph.getMetaValue("NuXL:NA"); - auto it = name2mod.find(NA); - if (it != name2mod.end()) - { - xl = it->second; - } - else - { - xl = new ResidueModification(); - xl->setFullId(NA); - xl->setOrigin('X'); // any AA - name2mod[NA] = xl; - } - - for (auto& ph_evidence : ph_evidences) - { - const String& acc = ph_evidence.getProteinAccession(); - const int peptide_start_in_protein = ph_evidence.getStart(); - - if (peptide_start_in_protein < 0) continue; - - const int xl_pos_in_protein = peptide_start_in_protein + best_localization; - - bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); - - // not localized? annotate region - if (best_localization < 0) - { - ModifiedRegion mr; - mr.xl = xl; - mr.first = ph_evidence.getStart(); - mr.last = ph_evidence.getEnd(); - if (is_target) - { - modified_region_xls_targets[acc][mr]++; - } - else - { - modified_region_xls_decoys[acc][mr]++; - } - } - - // retrieve protein the evidence points to - ProteinHit* protein = is_target ? acc2protein_targets[acc] : acc2protein_decoys[acc]; - if (xl_pos_in_protein < protein->getSequence().size()) - { - auto mods = protein->getModifications(); // TODO: add mutable reference access - mods.AALevelSummary[xl_pos_in_protein][xl].count++; - protein->setModifications(mods); - } - } - } - - map aa2protein_count_targets; // how many proteins have that AA cross-linked - map aa2psm_count_targets; // how many PSMs have that AA cross-linked - map aa2protein_count_decoys; // how many proteins have that AA cross-linked - map aa2psm_count_decoys; // how many PSMs have that AA cross-linked - - map aa2background_freq; // AA background distribution for normalization - - for (const ProteinIdentification& prot_id : prot_ids) - { - const vector& phs = prot_id.getHits(); - for (const ProteinHit& protein : phs) - { // for all identified proteins - const String& acc = protein.getAccession(); - bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); - - if (!is_target && !report_decoys) continue; // skip decoys if option is set - - const String& seq = protein.getSequence(); - - for (const char c : seq) { aa2background_freq[c] += 1.0; } - tsv_file.addLine(acc); - - auto mods = protein.getModifications(); - - // count how many PSMs support XL-ed position in the current protein - map position2psm_count; - for (const auto& p2ms : mods.AALevelSummary) - { - size_t position = p2ms.first; - for (const auto& m2s : p2ms.second) - { - const auto stat = m2s.second; - position2psm_count[position] += stat.count; - } - } - - // put string with AA, position, PSM count in sequence: e.g.: [Y123,2] - String annotated_sequence; - size_t p{0}; - - if (!position2psm_count.empty()) - { - for (const auto p2psm : position2psm_count) - { - while (p < p2psm.first) { annotated_sequence += seq[p]; ++p; } - // p now points to the modified AA - annotated_sequence += String("[") + seq[p] + String(p2psm.first + 1) + "," + String(p2psm.second) + "]"; - ++p; - } - while (p < seq.size()) { annotated_sequence += seq[p]; ++p; } // output AAs after last modification - - tsv_file.addLine(annotated_sequence); - } - else - { - tsv_file.addLine(seq); - } - - // output modification AA and count for this protein - tsv_file.addLine("Cross-link localizations:"); - set already_counted_at_protein_level; - for (const auto& p2ms : mods.AALevelSummary) - { - size_t position = p2ms.first; - - // retrieve AA a xl position - char AA_at_position = '?'; - if (seq.size() > position) - { - AA_at_position = seq[position]; - } - - // count a modified AA only once per protein for protein count - if (already_counted_at_protein_level.count(AA_at_position) == 0) - { - if (is_target) - { - aa2protein_count_targets[AA_at_position]++; - } - else - { - aa2protein_count_decoys[AA_at_position]++; - } - already_counted_at_protein_level.insert(AA_at_position); - } - - for (const auto& m2s : p2ms.second) - { - auto stat = m2s.second; - size_t count = stat.count; - if (is_target) - { - aa2psm_count_targets[AA_at_position] += count; - } - else - { - aa2psm_count_decoys[AA_at_position] += count; - } - tsv_file.addLine(m2s.first->getFullId() + ":" + AA_at_position + String(position + 1) + "(" + String(count) + ")"); - } - } - - // output list of modified regions (without AA level localization) - tsv_file.addLine("Cross-linked peptides without localization at single AA-level:"); - for (const auto& p2xlregions : modified_region_xls_targets) - { - for (const auto& region : p2xlregions.second) - { - const ModifiedRegion& r = region.first; - const size_t count = region.second; - tsv_file.addLine(r.xl->getFullId() + ":" + String(r.first + 1) + "-" + String(r.last + 1) + "(" + String(count) + ")"); - } - } - } - } - - double sum{}; - for (const auto& m : aa2background_freq) { sum += m.second; } - for (auto& m : aa2background_freq) { m.second /= sum; } - - if (report_decoys) - { - tsv_file.addLine("============================================================="); - tsv_file.addLine("Protein summary for decoy proteins:"); - tsv_file.addLine("AA:proteins"); - for (const auto& a2p : aa2protein_count_decoys) - { - tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); - } - - tsv_file.addLine("============================================================="); - tsv_file.addLine("PSM summary for decoy PSMs:"); - tsv_file.addLine("AA:PSMs"); - for (const auto& a2p : aa2psm_count_decoys) - { - tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second)); - } - } - - tsv_file.addLine("============================================================="); - tsv_file.addLine("Protein summary for target proteins:"); - tsv_file.addLine("AA:proteins"); - for (const auto& a2p : aa2protein_count_targets) - { - tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second) + "\tfreq. normalized: " + String(a2p.second * aa2background_freq[a2p.first])); - } - - tsv_file.addLine("============================================================="); - tsv_file.addLine("PSM summary for target PSMs:"); - tsv_file.addLine("AA:PSMs"); - for (const auto& a2p : aa2psm_count_targets) - { - tsv_file.addLine(String(a2p.first) + " : " + String(a2p.second) + "\tfreq. normalized: " + String(a2p.second * aa2background_freq[a2p.first])); - } - - for (auto m : name2mod) { delete(m.second); } // free memory - } - void filterPeakInterference_(PeakMap& spectra, const map& purities, double fragment_mass_tolerance = 20.0, bool fragment_mass_tolerance_unit_ppm = true) { double filtered_peaks_count{0}; @@ -5387,9 +4363,9 @@ static void scoreXLIons_( // preallocate storage for PSMs vector nr_candidates(spectra.size(), 0); - vector > annotated_XLs(spectra.size(), vector()); + vector > annotated_XLs(spectra.size(), vector()); for (auto & a : annotated_XLs) { a.reserve(2 * report_top_hits); } - vector > annotated_peptides(spectra.size(), vector()); + vector > annotated_peptides(spectra.size(), vector()); for (auto & a : annotated_peptides) { a.reserve(2 * report_top_hits); } #ifdef _OPENMP // locking is done at the spectrum level to ensure good parallelisation @@ -5423,9 +4399,6 @@ static void scoreXLIons_( digestor.setEnzyme(getStringOption_("peptide:enzyme")); digestor.setMissedCleavages(0); // for decoy generation disable missed cleavages - DecoyGenerator dg; - dg.setSeed(4711); - // append decoy proteins const size_t old_size = fasta_db.size(); for (size_t i = 0; i != old_size; ++i) @@ -5448,6 +4421,8 @@ static void scoreXLIons_( // switch cleavage sites (like in Andromeda or DecoyPyrate) // if (s.size() >= 2) std::swap(s[s.size() - 1], s[s.size() - 2]); + DecoyGenerator dg; // important to create inside the loop with same seed. Otherwise same peptides end up creating different decoys -> much more decoys than targets + dg.setSeed(4711); e.sequence += dg.shufflePeptides(aas, enzyme).toUnmodifiedString(); } e.identifier = "DECOY_" + e.identifier; @@ -5476,6 +4451,7 @@ static void scoreXLIons_( Size max_peptide_length = (Size)getIntOption_("peptide:max_size"); Size count_proteins(0), count_peptides(0); + Size count_decoy_peptides(0), count_target_peptides(0); #ifdef _OPENMP #pragma omp parallel for schedule(guided) @@ -5496,7 +4472,7 @@ static void scoreXLIons_( auto const & current_fasta_entry = fasta_db[fasta_index]; - bool is_decoy = current_fasta_entry.identifier.hasPrefix("DECOY_"); + bool is_decoy = current_fasta_entry.identifier[5] == '_'; // faster check than current_fasta_entry.identifier.hasPrefix("DECOY_") digestor.digestUnmodified(current_fasta_entry.sequence, current_digest, min_peptide_length, max_peptide_length); @@ -5525,6 +4501,21 @@ static void scoreXLIons_( #endif ++count_peptides; + if (is_decoy) + { +#ifdef _OPENMP +#pragma omp atomic +#endif + ++count_decoy_peptides; + } + else + { +#ifdef _OPENMP +#pragma omp atomic +#endif + ++count_target_peptides; + } + const String unmodified_sequence = cit->getString(); // only process peptides without ambiguous amino acids (placeholder / any amino acid) @@ -5609,7 +4600,7 @@ static void scoreXLIons_( #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag - if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } + if (exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX][0] == 0) { continue; } #endif // count candidate for spectrum @@ -5640,7 +4631,7 @@ static void scoreXLIons_( vector peak_matched(exp_spectrum.size(), false); scorePeptideIons_( exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], total_loss_template_z1_b_ions, total_loss_template_z1_y_ions, current_peptide_mass_without_NA, @@ -5672,7 +4663,7 @@ static void scoreXLIons_( const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); // add peptide hit - AnnotatedHit ah; + RNPxlAnnotatedHit ah; ah.NA_adduct_amb_index = NA_adduct_amb_index; // store index the entry in the set of ambiguous precursor adducts ah.mass_error_p = mass_error_score; ah.sequence = *cit; // copy StringView @@ -5715,7 +4706,7 @@ static void scoreXLIons_( ah.tag_shifted = longest_tags.tag_shifted; // combined score - const double tags = exp_spectrum.getFloatDataArrays()[1][0]; + const double tags = exp_spectrum.getFloatDataArrays()[2][0]; ah.n_theoretical_peaks = n_theoretical_peaks; ah.score = OpenNuXL::calculateCombinedScore(ah, false, tags); //ah.score = OpenNuXL::calculateFastScore(ah); does this work too @@ -5739,7 +4730,7 @@ static void scoreXLIons_( // prevent vector from growing indefinitly (memory) but don't shrink the vector every time if (annotated_peptides[scan_index].size() >= 2 * report_top_hits) { - std::partial_sort(annotated_peptides[scan_index].begin(), annotated_peptides[scan_index].begin() + report_top_hits, annotated_peptides[scan_index].end(), AnnotatedHit::hasBetterScore); + std::partial_sort(annotated_peptides[scan_index].begin(), annotated_peptides[scan_index].begin() + report_top_hits, annotated_peptides[scan_index].end(), RNPxlAnnotatedHit::hasBetterScore); annotated_peptides[scan_index].resize(report_top_hits); } } @@ -5773,6 +4764,13 @@ static void scoreXLIons_( const char& cross_linked_nucleotide = nuc_2_adducts.first; const vector& partial_loss_modification = nuc_2_adducts.second; + // e.g., a precursor adduct of T-C4H5N3O1 is not feasible as it would lead to N(-1). T + // This should be filtered out during generation of feasible fragment adducts. + // This is just a safeguard to prevent regression. + assert(!partial_loss_modification.empty()); + + if (partial_loss_modification.empty()) cout << "Error: empty partial loss modification" << endl; + PeakSpectrum marker_ions_sub_score_spectrum_z1; // add shifted marker ions of charge 1 marker_ions_sub_score_spectrum_z1.getStringDataArrays().resize(1); // annotation @@ -5780,7 +4778,7 @@ static void scoreXLIons_( RNPxlFragmentIonGenerator::addMS2MarkerIons( marker_ions, marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX], + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], marker_ions_sub_score_spectrum_z1.getStringDataArrays()[0]); // nucleotide is associated with certain NA-related fragment losses? @@ -5798,9 +4796,10 @@ static void scoreXLIons_( ////////////////////////////////////////// // ID-Filter if (skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) { continue; } - #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT + +#ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag - if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } + if (exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX][0] == 0) { continue; } #endif #ifdef _OPENMP @@ -5832,7 +4831,7 @@ static void scoreXLIons_( scorePeptideIons_( exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], total_loss_template_z1_b_ions, total_loss_template_z1_y_ions, current_peptide_mass_without_NA, @@ -5856,8 +4855,6 @@ static void scoreXLIons_( const double tlss_total_MIC = tlss_MIC + im_MIC + (pc_MIC - floor(pc_MIC)); - // total_loss_score = total_loss_score - 0.22 * (double)cit->size(); - if (badTotalLossScore(total_loss_score, tlss_Morph, tlss_modds, tlss_total_MIC)) { continue; } vector intensity_xls(total_loss_template_z1_b_ions.size(), 0.0); @@ -5908,7 +4905,7 @@ static void scoreXLIons_( const double mass_error_score = pdf(gaussian_mass_error, mass_error_ppm) / pdf(gaussian_mass_error, 0.0); // add peptide hit - AnnotatedHit ah; + RNPxlAnnotatedHit ah; ah.NA_adduct_amb_index = NA_adduct_amb_index; // store index the entry in the set of ambiguous precursor adducts ah.mass_error_p = mass_error_score; @@ -5973,7 +4970,7 @@ static void scoreXLIons_( ah.tag_shifted = longest_tags.tag_shifted; // combined score - const double tags = exp_spectrum.getFloatDataArrays()[1][0]; + const double tags = exp_spectrum.getFloatDataArrays()[2][0]; ah.n_theoretical_peaks = n_theoretical_peaks; ah.score = OpenNuXL::calculateCombinedScore(ah, true, tags); @@ -5996,7 +4993,7 @@ static void scoreXLIons_( // prevent vector from growing indefinitly (memory) but don't shrink the vector every time if (annotated_XLs[scan_index].size() >= 2 * report_top_hits) { - std::partial_sort(annotated_XLs[scan_index].begin(), annotated_XLs[scan_index].begin() + report_top_hits, annotated_XLs[scan_index].end(), AnnotatedHit::hasBetterScore); + std::partial_sort(annotated_XLs[scan_index].begin(), annotated_XLs[scan_index].begin() + report_top_hits, annotated_XLs[scan_index].end(), RNPxlAnnotatedHit::hasBetterScore); annotated_XLs[scan_index].resize(report_top_hits); } } @@ -6022,7 +5019,7 @@ static void scoreXLIons_( #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT // require at least one mass tag - if (exp_spectrum.getIntegerDataArrays()[IA_DENOVO_TAG_INDEX][0] == 0) { continue; } + if (exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_DENOVO_TAG_INDEX][0] == 0) { continue; } #endif #ifdef _OPENMP omp_set_lock(&(annotated_peptides_lock[scan_index])); @@ -6066,6 +5063,8 @@ static void scoreXLIons_( OPENMS_LOG_INFO << "Proteins: " << count_proteins << endl; OPENMS_LOG_INFO << "Peptides: " << count_peptides << endl; + OPENMS_LOG_INFO << "Peptides (targets): " << count_target_peptides << endl; + OPENMS_LOG_INFO << "Peptides (decoys): " << count_decoy_peptides << endl; OPENMS_LOG_INFO << "Processed peptides: " << processed_petides.size() << endl; vector peptide_ids; @@ -6469,7 +5468,7 @@ static void scoreXLIons_( out2 = out_tsv; out2.substitute(".tsv", "_proteins"); TextFile tsv_file; - annotateProteinModificationForTopHits_(tmp_prots, xl_pi, tsv_file); + RNPxlProteinReport::annotateProteinModificationForTopHits(tmp_prots, xl_pi, tsv_file); tsv_file.store(out2 + String::number(xlFDR, 4) + "_XLs.tsv"); } } @@ -6600,7 +5599,7 @@ static void scoreXLIons_( out2 = out_tsv; out2.substitute(".tsv", "_perc_proteins"); TextFile tsv_file; - annotateProteinModificationForTopHits_(tmp_prots, xl_pi, tsv_file); + RNPxlProteinReport::annotateProteinModificationForTopHits(tmp_prots, xl_pi, tsv_file); tsv_file.store(out2 + String::number(xlFDR, 4) + "_XLs.tsv"); } } @@ -6659,12 +5658,12 @@ static void scoreXLIons_( if (!marker_ions_sub_score_spectrum_z1.empty()) { - auto const & r = MorpheusScore::compute(fragment_mass_tolerance, + auto const & r = MorpheusScore::compute(fragment_mass_tolerance * 2.0, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], marker_ions_sub_score_spectrum_z1, - marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[IA_CHARGE_INDEX]); + marker_ions_sub_score_spectrum_z1.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX]); marker_ions_sub_score = r.TIC != 0 ? r.MIC / r.TIC : 0; } @@ -6679,17 +5678,17 @@ static void scoreXLIons_( partial_loss_sub_score = HyperScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], *pl_spec, - pl_spec->getIntegerDataArrays()[IA_CHARGE_INDEX], + pl_spec->getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], intensity_sum); auto const & pl_sub_scores = MorpheusScore::compute(fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, exp_spectrum, - exp_spectrum.getIntegerDataArrays()[IA_CHARGE_INDEX], + exp_spectrum.getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX], *pl_spec, - pl_spec->getIntegerDataArrays()[IA_CHARGE_INDEX]); + pl_spec->getIntegerDataArrays()[RNPxlConstants::IA_CHARGE_INDEX]); plss_MIC = pl_sub_scores.TIC != 0 ? pl_sub_scores.MIC / pl_sub_scores.TIC : 0; plss_Morph = pl_sub_scores.score; const float fragment_mass_tolerance_Da = 2.0 * fragment_mass_tolerance * 1e-6 * 1000.0; @@ -6697,16 +5696,22 @@ static void scoreXLIons_( // if we only have 1 peak assume some kind of average error to not underestimate the real error to much // plss_err = plss_Morph > 2 ? pl_sub_scores.err_ppm : fragment_mass_tolerance; + const double p_random_match = exp_spectrum.getFloatDataArrays()[1][0]; + plss_modds = matchOddsScore_(pl_spec->size(), (int)plss_Morph, p_random_match); +/* plss_modds = matchOddsScore_(pl_spec->size(), fragment_mass_tolerance_Da, exp_spectrum.size(), exp_spectrum.back().getMZ(), (int)plss_Morph); +*/ } #ifdef DEBUG_OpenNuXL OPENMS_LOG_DEBUG << "scan index: " << scan_index << " achieved score: " << score << endl; #endif } + + }; #ifdef FILTER_AMBIGIOUS_PEAKS From e8fc34cd0cd6cae19e3ca314613203be4538aed2 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 29 Dec 2020 09:10:44 +0100 Subject: [PATCH 154/471] factored FDR code out into class --- .../include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h | 71 ++++++++ .../OpenMS/ANALYSIS/RNPXL/sources.cmake | 1 + src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp | 144 +++++++++++++++ .../source/ANALYSIS/RNPXL/sources.cmake | 1 + src/utils/OpenNuXL.cpp | 166 ++---------------- 5 files changed, 232 insertions(+), 151 deletions(-) create mode 100644 src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h create mode 100644 src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h new file mode 100644 index 00000000000..e706796761d --- /dev/null +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h @@ -0,0 +1,71 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2020. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#pragma once + +#include +#include +#include +#include +#include +#include + +namespace OpenMS +{ + +/// @brief adapted FDR calculation for NA cross-links +class OPENMS_DLLAPI RNPxlFDR +{ + public: + explicit RNPxlFDR(size_t report_top_hits); + + // calculate PSM-level q-values (irrespective of XL/non-XL class) + void QValueAtPSMLevel(std::vector& peptide_ids) const; + + // calculate PSM-level q-values for XL and non-XL class separately. + void PeptideAndXLQValueAtPSMLevel( + const std::vector& protein_ids, + const std::vector& peptide_ids, + std::vector& pep, + double peptide_PSM_qvalue_threshold, + std::vector& xl, + std::vector xl_PSM_qvalue_thresholds, + const String& out_idxml) const; + private: + size_t report_top_hits_; +}; + +} + + diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake b/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake index 574599c7ade..5ba10567519 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/sources.cmake @@ -10,6 +10,7 @@ PScore.h RNPxlAnnotateAndLocate.h RNPxlAnnotatedHit.h RNPxlConstants.h +RNPxlFDR.h RNPxlFragmentAdductDefinition.h RNPxlFragmentAnnotationHelper.h RNPxlFragmentIonGenerator.h diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp new file mode 100644 index 00000000000..9ebb3603f90 --- /dev/null +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp @@ -0,0 +1,144 @@ +// -------------------------------------------------------------------------- +// OpenMS -- Open-Source Mass Spectrometry +// -------------------------------------------------------------------------- +// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, +// ETH Zurich, and Freie Universitaet Berlin 2002-2020. +// +// This software is released under a three-clause BSD license: +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of any author or any participating institution +// may be used to endorse or promote products derived from this software +// without specific prior written permission. +// For a full list of authors, refer to the file AUTHORS. +// -------------------------------------------------------------------------- +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING +// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#include +#include +#include +#include +#include + +using namespace std; + +namespace OpenMS +{ + RNPxlFDR::RNPxlFDR(size_t report_top_hits): + report_top_hits_(report_top_hits) + { + } + + void RNPxlFDR::QValueAtPSMLevel(vector& peptide_ids) const + { + FalseDiscoveryRate fdr; + Param p = fdr.getParameters(); + p.setValue("add_decoy_proteins", "true"); // we still want decoys in the result (e.g., to run percolator) + p.setValue("add_decoy_peptides", "true"); + if (report_top_hits_ >= 2) + { + p.setValue("use_all_hits", "true"); + } + fdr.setParameters(p); + fdr.apply(peptide_ids); + } + + void RNPxlFDR::PeptideAndXLQValueAtPSMLevel( + const vector& protein_ids, + const vector& peptide_ids, + vector& pep_pi, + double peptide_PSM_qvalue_threshold, + vector& xl_pi, + vector xl_PSM_qvalue_thresholds, + const String& out_idxml) const + { + FalseDiscoveryRate fdr; + Param p = fdr.getParameters(); + p.setValue("add_decoy_proteins", "true"); // we still want decoys in the result (e.g., to run percolator) + p.setValue("add_decoy_peptides", "true"); + if (report_top_hits_ >= 2) + { + p.setValue("use_all_hits", "true"); + } + fdr.setParameters(p); + + for (const auto & pi : peptide_ids) + { + vector pep_ph, xl_ph; + for (const auto & ph : pi.getHits()) + { + if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) + { // only add best hit + if (pep_ph.empty() && xl_ph.empty()) pep_ph.push_back(ph); + } + else + { + if (pep_ph.empty() && xl_ph.empty()) xl_ph.push_back(ph); + } + } + if (!pep_ph.empty()) { pep_pi.push_back(pi); pep_pi.back().setHits(pep_ph); } + if (!xl_ph.empty()) { xl_pi.push_back(pi); xl_pi.back().setHits(xl_ph); } + } + + // calculate FDRs separately + fdr.apply(xl_pi); + fdr.apply(pep_pi); + + IDFilter::removeDecoyHits(xl_pi); + IDFilter::removeDecoyHits(pep_pi); + + if (peptide_PSM_qvalue_threshold > 0.0 && peptide_PSM_qvalue_threshold < 1.0) + { + IDFilter::filterHitsByScore(pep_pi, peptide_PSM_qvalue_threshold); + } + + { + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, pep_pi); + IdXMLFile().store(out_idxml + String::number(peptide_PSM_qvalue_threshold, 4) + "_peptides.idXML", tmp_prots, pep_pi); + } + + // treat disabled filtering as 100% FDR + std::replace(xl_PSM_qvalue_thresholds.begin(), xl_PSM_qvalue_thresholds.end(), 0.0, 1.0); + std::sort(xl_PSM_qvalue_thresholds.begin(), xl_PSM_qvalue_thresholds.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters + for (double xlFDR : xl_PSM_qvalue_thresholds) + { + OPENMS_LOG_INFO << "Writing XL results at xl-FDR: " << xlFDR << endl; + if (xlFDR > 0.0 && xlFDR < 1.0) + { + IDFilter::filterHitsByScore(xl_pi, xlFDR); + } + { + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); + // PSM result + IdXMLFile().store(out_idxml + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); + + // protein result + TextFile tsv_file; + RNPxlProteinReport::annotateProteinModificationForTopHits(tmp_prots, xl_pi, tsv_file); + tsv_file.store(out_idxml + "_proteins" + String::number(xlFDR, 4) + "_XLs.tsv"); + } + } + } + +} // namespace + diff --git a/src/openms/source/ANALYSIS/RNPXL/sources.cmake b/src/openms/source/ANALYSIS/RNPXL/sources.cmake index 0c1a3c5c8e9..2d3ca70d457 100644 --- a/src/openms/source/ANALYSIS/RNPXL/sources.cmake +++ b/src/openms/source/ANALYSIS/RNPXL/sources.cmake @@ -8,6 +8,7 @@ ModifiedPeptideGenerator.cpp MorpheusScore.cpp PScore.cpp RNPxlAnnotateAndLocate.cpp +RNPxlFDR.cpp RNPxlFragmentAdductDefinition.cpp RNPxlFragmentAnnotationHelper.cpp RNPxlFragmentIonGenerator.cpp diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 98b1dc2bf57..8fee6053554 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -61,6 +61,7 @@ #include #include #include +#include #include #include #include @@ -1519,7 +1520,7 @@ score += ah.mass_error_p * 1.15386068 + 28.09 * (ah.tag_shifted >= 1); */ - return ah.modds + 0.00001 * ah.pl_modds; + return ah.modds + ah.pl_modds; //return sqrt(ah.pl_modds*ah.pl_modds + ah.modds*ah.modds); /* const double ret = 1.0 * ah.total_loss_score @@ -4207,16 +4208,7 @@ static void scoreXLIons_( // calculate all feasible fragment adducts from all possible precursor adducts RNPxlParameterParsing::PrecursorsToMS2Adducts all_feasible_fragment_adducts = RNPxlParameterParsing::getAllFeasibleFragmentAdducts(mm, nucleotide_to_fragment_adducts, can_xl_); - // calculate FDR - FalseDiscoveryRate fdr; - Param p = fdr.getParameters(); - p.setValue("add_decoy_proteins", "true"); // we still want decoys in the result (e.g., to run percolator) - p.setValue("add_decoy_peptides", "true"); - if (report_top_hits >= 2) - { - p.setValue("use_all_hits", "true"); - } - fdr.setParameters(p); + RNPxlFDR fdr(report_top_hits); // load MS2 map PeakMap spectra; @@ -5372,7 +5364,8 @@ static void scoreXLIons_( cout << "Imputed XL features in " << imputed << " linear peptides." << endl; } - fdr.apply(peptide_ids); + // q-value at PSM level irrespective of class (XL/non-XL) + fdr.QValueAtPSMLevel(peptide_ids); // write ProteinIdentifications and PeptideIdentifications to IdXML IdXMLFile().store(out_idxml, protein_ids, peptide_ids); @@ -5404,76 +5397,11 @@ static void scoreXLIons_( IDFilter::removeUnreferencedProteins(protein_ids, peptide_ids); // split PSMs into XLs and non-XLs but keep only best one of both - vector pep_pi; - vector xl_pi; - for (const auto & pi : peptide_ids) - { - vector pep_ph; - vector xl_ph; - for (const auto & ph : pi.getHits()) - { - if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) - { // only add best hit - if (pep_ph.empty() && xl_ph.empty()) pep_ph.push_back(ph); - } - else - { - if (pep_ph.empty() && xl_ph.empty()) xl_ph.push_back(ph); - } - } - if (!pep_ph.empty()) { pep_pi.push_back(pi); pep_pi.back().setHits(pep_ph); } - if (!xl_ph.empty()) { xl_pi.push_back(pi); xl_pi.back().setHits(xl_ph); } - } - - // calculate FDRs separately - fdr.apply(xl_pi); - fdr.apply(pep_pi); - - IDFilter::removeDecoyHits(xl_pi); - IDFilter::removeDecoyHits(pep_pi); - - if (peptide_FDR > 0.0 && peptide_FDR < 1.0) - { - IDFilter::filterHitsByScore(pep_pi, peptide_FDR); - } - - { - String out2(out_idxml); - out2.substitute(".idXML", "_"); - vector tmp_prots = protein_ids; - IDFilter::removeUnreferencedProteins(tmp_prots, pep_pi); - IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", tmp_prots, pep_pi); - } + vector pep_pi, xl_pi; + String original_PSM_output_filename(out_idxml); + original_PSM_output_filename.substitute(".idXML", "_"); + fdr.PeptideAndXLQValueAtPSMLevel(protein_ids, peptide_ids, pep_pi, peptide_FDR, xl_pi, XL_FDR, original_PSM_output_filename); - std::replace(XL_FDR.begin(), XL_FDR.end(), 0.0, 1.0); - sort(XL_FDR.begin(), XL_FDR.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters - for (double xlFDR : XL_FDR) - { - OPENMS_LOG_INFO << "Writing XL results at xl-FDR: " << xlFDR << endl; - if (xlFDR > 0.0 && xlFDR < 1.0) - { - IDFilter::filterHitsByScore(xl_pi, xlFDR); - } - { - String out2(out_idxml); - out2.substitute(".idXML", "_"); - vector tmp_prots = protein_ids; - IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); - // PSM result - IdXMLFile().store(out2 + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); - - // protein result - if (!out_tsv.empty()) - { - out2 = out_tsv; - out2.substitute(".tsv", "_proteins"); - TextFile tsv_file; - RNPxlProteinReport::annotateProteinModificationForTopHits(tmp_prots, xl_pi, tsv_file); - tsv_file.store(out2 + String::number(xlFDR, 4) + "_XLs.tsv"); - } - } - } - String percolator_executable = getStringOption_("percolator_executable"); bool sufficient_PSMs_for_score_recalibration = (xl_pi.size() + pep_pi.size()) > 1000; if (!percolator_executable.empty() && sufficient_PSMs_for_score_recalibration) // only try to call percolator if we have some PSMs @@ -5519,7 +5447,7 @@ static void scoreXLIons_( IDFilter::keepNBestHits(peptide_ids, 1); IDFilter::removeUnreferencedProteins(protein_ids, peptide_ids); - // annotate RNPxl related information to hits and create report + // annotate RNPxl related information to hits and create report vector csv_rows_percolator = RNPxlReport::annotate(spectra, peptide_ids, meta_values_to_export, marker_ions_tolerance); // save report @@ -5535,75 +5463,11 @@ static void scoreXLIons_( csv_file.store(out_percolator_tsv); } - - // split PSMs into XLs and non-XLs but keep only best one of both - vector pep_pi; - vector xl_pi; - for (const auto & pi : peptide_ids) - { - vector pep_ph, xl_ph; - for (const auto & ph : pi.getHits()) - { - if (static_cast(ph.getMetaValue("NuXL:isXL")) == 0) - { // only add best hit - if (pep_ph.empty() && xl_ph.empty()) pep_ph.push_back(ph); - } - else - { - if (pep_ph.empty() && xl_ph.empty()) xl_ph.push_back(ph); - } - } - if (!pep_ph.empty()) { pep_pi.push_back(pi); pep_pi.back().setHits(pep_ph); } - if (!xl_ph.empty()) { xl_pi.push_back(pi); xl_pi.back().setHits(xl_ph); } - } - - // calculate FDRs separately - fdr.apply(xl_pi); - fdr.apply(pep_pi); - - IDFilter::removeDecoyHits(xl_pi); - IDFilter::removeDecoyHits(pep_pi); - - if (peptide_FDR > 0.0 && peptide_FDR < 1.0) - { - IDFilter::filterHitsByScore(pep_pi, peptide_FDR); - } - { - String out2(out_idxml); - out2.substitute(".idXML", "_perc_"); - vector tmp_prots = protein_ids; - IDFilter::removeUnreferencedProteins(tmp_prots, pep_pi); - IdXMLFile().store(out2 + String::number(peptide_FDR, 4) + "_peptides.idXML", tmp_prots, pep_pi); - } - - std::replace(XL_FDR.begin(), XL_FDR.end(), 0.0, 1.0); // treat disabled filtering as 100% FDR - sort(XL_FDR.begin(), XL_FDR.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters - for (double xlFDR : XL_FDR) - { - OPENMS_LOG_INFO << "Writing XL results at xl-FDR: " << xlFDR << endl; - if (xlFDR > 0.0 && xlFDR < 1.0) - { - IDFilter::filterHitsByScore(xl_pi, xlFDR); - } - { - String out2(out_idxml); - out2.substitute(".idXML", "_perc_"); - vector tmp_prots = protein_ids; - IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); - - // store PSM results - IdXMLFile().store(out2 + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); - // store protein results - if (!out_tsv.empty()) - { - out2 = out_tsv; - out2.substitute(".tsv", "_perc_proteins"); - TextFile tsv_file; - RNPxlProteinReport::annotateProteinModificationForTopHits(tmp_prots, xl_pi, tsv_file); - tsv_file.store(out2 + String::number(xlFDR, 4) + "_XLs.tsv"); - } - } - } + vector pep_pi, xl_pi; + + String percolator_PSM_output_filename(out_idxml); + percolator_PSM_output_filename.substitute(".idXML", "_perc_"); + fdr.PeptideAndXLQValueAtPSMLevel(protein_ids, peptide_ids, pep_pi, peptide_FDR, xl_pi, XL_FDR, percolator_PSM_output_filename); } } else From 209e8fd7d4e635a22992b2accf1ec59e42e190c8 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Fri, 1 Jan 2021 10:05:12 +0100 Subject: [PATCH 155/471] added presets --- .../include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h | 16 +- src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp | 124 +++++--- src/utils/OpenNuXL.cpp | 268 ++++++++++++++++-- 3 files changed, 352 insertions(+), 56 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h index e706796761d..eb8f92f0008 100644 --- a/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h +++ b/src/openms/include/OpenMS/ANALYSIS/RNPXL/RNPxlFDR.h @@ -50,11 +50,25 @@ class OPENMS_DLLAPI RNPxlFDR public: explicit RNPxlFDR(size_t report_top_hits); + // split by meta value "NuXL:isXL" == 0 + void splitIntoPeptidesAndXLs(const std::vector& peptide_ids, + std::vector& pep_pi, + std::vector& xl_pi) const; + + void mergePeptidesAndXLs(const std::vector& pep_pi, + const std::vector& xl_pi, + std::vector& peptide_ids) const; + // calculate PSM-level q-values (irrespective of XL/non-XL class) void QValueAtPSMLevel(std::vector& peptide_ids) const; // calculate PSM-level q-values for XL and non-XL class separately. - void PeptideAndXLQValueAtPSMLevel( + void calculatePeptideAndXLQValueAtPSMLevel(const std::vector& peptide_ids, + std::vector& pep_pi, + std::vector& xl_pi) const; + + // calculate separate FDRs, filter decoys, write PSM and protein reports + void calculatePeptideAndXLQValueAndFilterAtPSMLevel( const std::vector& protein_ids, const std::vector& peptide_ids, std::vector& pep, diff --git a/src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp b/src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp index 9ebb3603f90..1fbfc328871 100644 --- a/src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp +++ b/src/openms/source/ANALYSIS/RNPXL/RNPxlFDR.cpp @@ -61,25 +61,8 @@ namespace OpenMS fdr.apply(peptide_ids); } - void RNPxlFDR::PeptideAndXLQValueAtPSMLevel( - const vector& protein_ids, - const vector& peptide_ids, - vector& pep_pi, - double peptide_PSM_qvalue_threshold, - vector& xl_pi, - vector xl_PSM_qvalue_thresholds, - const String& out_idxml) const + void RNPxlFDR::splitIntoPeptidesAndXLs(const vector& peptide_ids, vector& pep_pi, vector& xl_pi) const { - FalseDiscoveryRate fdr; - Param p = fdr.getParameters(); - p.setValue("add_decoy_proteins", "true"); // we still want decoys in the result (e.g., to run percolator) - p.setValue("add_decoy_peptides", "true"); - if (report_top_hits_ >= 2) - { - p.setValue("use_all_hits", "true"); - } - fdr.setParameters(p); - for (const auto & pi : peptide_ids) { vector pep_ph, xl_ph; @@ -97,11 +80,73 @@ namespace OpenMS if (!pep_ph.empty()) { pep_pi.push_back(pi); pep_pi.back().setHits(pep_ph); } if (!xl_ph.empty()) { xl_pi.push_back(pi); xl_pi.back().setHits(xl_ph); } } + } + + void RNPxlFDR::mergePeptidesAndXLs(const vector& pep_pi, const vector& xl_pi, vector& peptide_ids) const + { + peptide_ids.clear(); + map native_id_to_id_index; + size_t id_index = 0; + for (const auto & pi : pep_pi) + { + peptide_ids.push_back(pi); + native_id_to_id_index[pi.getMetaValue("spectrum_reference")] = id_index; + ++id_index; + } + for (const auto & pi : xl_pi) + { + if (native_id_to_id_index.find(pi.getMetaValue("spectrum_reference")) == native_id_to_id_index.end()) + { + peptide_ids.push_back(pi); + } + else + { + // spectrum already identified + size_t index = native_id_to_id_index.at(pi.getMetaValue("spectrum_reference")); + auto hits = peptide_ids[index].getHits(); + for (auto h : pi.getHits()) + { + hits.push_back(h); + } + peptide_ids[index].setHits(hits); + peptide_ids[index].assignRanks(); + } + } + } + + void RNPxlFDR::calculatePeptideAndXLQValueAtPSMLevel(const vector& peptide_ids, vector& pep_pi, vector& xl_pi) const + { + FalseDiscoveryRate fdr; + Param p = fdr.getParameters(); + p.setValue("add_decoy_proteins", "true"); // we still want decoys in the result (e.g., to run percolator) + p.setValue("add_decoy_peptides", "true"); + if (report_top_hits_ >= 2) + { + p.setValue("use_all_hits", "true"); + } + fdr.setParameters(p); + + splitIntoPeptidesAndXLs(peptide_ids, pep_pi, xl_pi); + // calculate FDRs separately fdr.apply(xl_pi); fdr.apply(pep_pi); + } + + void RNPxlFDR::calculatePeptideAndXLQValueAndFilterAtPSMLevel( + const vector& protein_ids, + const vector& peptide_ids, + vector& pep_pi, + double peptide_PSM_qvalue_threshold, + vector& xl_pi, + vector xl_PSM_qvalue_thresholds, + const String& out_idxml) const + { + // calculate separate FDRs + calculatePeptideAndXLQValueAtPSMLevel(peptide_ids, pep_pi, xl_pi); + // filter IDFilter::removeDecoyHits(xl_pi); IDFilter::removeDecoyHits(pep_pi); @@ -110,33 +155,34 @@ namespace OpenMS IDFilter::filterHitsByScore(pep_pi, peptide_PSM_qvalue_threshold); } + // store peptide PSM result { vector tmp_prots = protein_ids; IDFilter::removeUnreferencedProteins(tmp_prots, pep_pi); IdXMLFile().store(out_idxml + String::number(peptide_PSM_qvalue_threshold, 4) + "_peptides.idXML", tmp_prots, pep_pi); } - // treat disabled filtering as 100% FDR - std::replace(xl_PSM_qvalue_thresholds.begin(), xl_PSM_qvalue_thresholds.end(), 0.0, 1.0); - std::sort(xl_PSM_qvalue_thresholds.begin(), xl_PSM_qvalue_thresholds.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters - for (double xlFDR : xl_PSM_qvalue_thresholds) - { - OPENMS_LOG_INFO << "Writing XL results at xl-FDR: " << xlFDR << endl; - if (xlFDR > 0.0 && xlFDR < 1.0) - { - IDFilter::filterHitsByScore(xl_pi, xlFDR); - } - { - vector tmp_prots = protein_ids; - IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); - // PSM result - IdXMLFile().store(out_idxml + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); - - // protein result - TextFile tsv_file; - RNPxlProteinReport::annotateProteinModificationForTopHits(tmp_prots, xl_pi, tsv_file); - tsv_file.store(out_idxml + "_proteins" + String::number(xlFDR, 4) + "_XLs.tsv"); - } + // treat disabled filtering as 100% FDR + std::replace(xl_PSM_qvalue_thresholds.begin(), xl_PSM_qvalue_thresholds.end(), 0.0, 1.0); + std::sort(xl_PSM_qvalue_thresholds.begin(), xl_PSM_qvalue_thresholds.end(), greater()); // important: sort by threshold (descending) to generate results by applying increasingly stringent q-value filters + for (double xlFDR : xl_PSM_qvalue_thresholds) + { + OPENMS_LOG_INFO << "Writing XL results at xl-FDR: " << xlFDR << endl; + if (xlFDR > 0.0 && xlFDR < 1.0) + { + IDFilter::filterHitsByScore(xl_pi, xlFDR); + } + + vector tmp_prots = protein_ids; + IDFilter::removeUnreferencedProteins(tmp_prots, xl_pi); + + // write out XL PSM result + IdXMLFile().store(out_idxml + String::number(xlFDR, 4) + "_XLs.idXML", tmp_prots, xl_pi); + + // write out XL protein result + TextFile tsv_file; + RNPxlProteinReport::annotateProteinModificationForTopHits(tmp_prots, xl_pi, tsv_file); + tsv_file.store(out_idxml + "proteins" + String::number(xlFDR, 4) + "_XLs.tsv"); } } diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 8fee6053554..3c4fc58df03 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -265,7 +265,170 @@ class OpenNuXL : protected: /// percolator feature set StringList feature_set_; - + + void applyPresets_(StringList& modifications, StringList& fragment_adducts, String& can_cross_link) + { + const String p = getStringOption_("RNPxl:presets"); + if (p == "RNA") + { + modifications = + {"U:", + "U:-H2O", + "U:-H2O-HPO3", + "U:-HPO3", + "C:", + "C:-NH3", + "C:-H2O", + "C:-NH3-HPO3", + "C:-H2O-HPO3", + "C:-HPO3", + "G:", + "G:-H2O", + "G:-NH3", + "G:-H2O-HPO3", + "G:-NH3-HPO3", + "G:-HPO3", + "A:", + "A:-NH3", + "A:-NH3-HPO3", + "A:-HPO3"}; + fragment_adducts = + {"U:C9H10N2O5;U-H3PO4", + "U:C4H4N2O2;U';", + "U:C4H2N2O1;U';-H2O", + "U:C3O;C3O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C5H9O7P;ribose", + "U:C5H7O6P;ribose-H2O", + "U:C5H6O3;ribose-H2O-HPO3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C4H5N3O;C';", + "C:C4H3N3;C';-H2O", + "C:C4H2N2O;C';-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H13N5O5;G-HPO3", + "C:C9H10N2O5;C-NH3-HPO3", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C5H5N5O;G';", + "G:C5H3N5;G';-H2O", + "G:C5H2N4O;G';-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C5H5N5;A';", + "A:C5H2N4;A';-NH3", + "C:C5H9O7P;ribose", + "G:C5H9O7P;ribose", + "A:C5H9O7P;ribose", + "G:C5H7O6P;rib-H2O", + "C:C5H7O6P;rib-H2O", + "A:C5H7O6P;rib-H2O", + "G:C5H6O3;ribose-H2O-HPO3", + "C:C5H6O3;ribose-H2O-HPO3", + "A:C5H6O3;ribose-H2O-HPO3"}; + can_cross_link = "UCGA"; + } + else if (p == "DNA") + { + modifications = { + "T:", + "T:-H2O", + "T:-H2O-HPO3", + "T:-HPO3", + "A:", + "A:-H2O", + "A:-H2O-HPO3", + "A:-HPO3", + "G:", + "G:-H2O", + "G:-NH3", + "A:-NH3", + "G:-HPO3", + "G:-H2O-HPO3", + "G:-NH3-HPO3", + "C:", + "C:-H2O", + "C:-NH3", + "C:-H2O-HPO3", + "C:-NH3", + "C:-NH3-HPO3", + "T:+C5H7O5P", + "A:+C5H7O5P", + "G:+C5H7O5P", + "C:+C5H7O5P", + "T:-C4H5N3O", + "A:-C5H5N5", + "T:+HPO3", + "C:+HPO3", + "A:+HPO3", + "G:+HPO3", + "T:+HPO3-H2O", + "C:+HPO3-H2O", + "A:+HPO3-H2O", + "G:+HPO3-H2O"}; + + fragment_adducts = { + "T:C10H15N2O8P;T", + "T:C10H13N2O7P;T-H2O", + "T:C10H14N2O5;T-HPO3", + "T:C10H12N2O4;T-H3PO4", + "T:C5H6N2O2;T';", + "T:C5H4N2O;T';-H2O", + "C:C9H14N3O7P;C", + "C:C9H11N2O7P;C-NH3", + "C:C9H12N3O6P;C-H2O", + "C:C9H13N3O4;C-HPO3", + "C:C9H11N3O3;C-H3PO4", + "C:C4H5N3O;C';", + "C:C4H3N3;C';-H2O", + "C:C4H2N2O;C';-NH3", + "G:C10H14N5O7P;G", + "G:C10H12N5O6P;G-H2O", + "G:C10H11N4O7P;G-NH3", + "G:C10H13N5O4;G-HPO3", + "C:C9H10N2O4;C-NH3-HPO3", + "G:C10H10N4O4;G-NH3-HPO3", + "G:C10H11N5O3;G-H3PO4", + "G:C5H5N5O;G';", + "G:C5H3N5;G';-H2O", + "G:C5H2N4O;G';-NH3", + "A:C10H14N5O6P;A", + "A:C10H12N5O5P;A-H2O", + "A:C10H11N4O6P;A-NH3", + "A:C10H13N5O3;A-HPO3", + "A:C10H11N5O2;A-H3PO4", + "A:C10H10N5O3;A-NH3-HPO3", + "A:C5H5N5;A';", + "A:C5H2N4;A';-NH3", + "A:C5H9O6P;dribose", + "G:C5H9O6P;dribose", + "C:C5H9O6P;dribose", + "T:C5H9O6P;dribose", + "A:C5H7O5P;dribose-H2O", + "G:C5H7O5P;dribose-H2O", + "C:C5H7O5P;dribose-H2O", + "T:C5H7O5P;dribose-H2O", + "A:C5H8O3;dribose-HPO3", + "G:C5H8O3;dribose-HPO3", + "C:C5H8O3;dribose-HPO3", + "T:C5H8O3;dribose-HPO3"}; + + can_cross_link = "CTGA"; + } + } + void registerOptionsAndFlags_() override { registerInputFile_("in", "", "", "input file "); @@ -345,6 +508,10 @@ class OpenNuXL : // RNPxl specific registerTOPPSubsection_("RNPxl", "RNPxl Options"); + + registerStringOption_("RNPxl:presets", " - + - 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@@ -309,12 +309,12 @@ 12050 - 24121 + 24221 - 34037 + 34137 -35481 +35581 0 \ No newline at end of file From 61f3ecd3df3e992217eba11a4f5a996212a6087d Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 8 Sep 2021 12:13:11 +0200 Subject: [PATCH 188/471] add feature augmentation --- src/utils/OpenNuXL.cpp | 186 ++++++++++++++--------------------------- 1 file changed, 64 insertions(+), 122 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index a927dcdfa3a..511d2d8cba7 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -55,7 +55,6 @@ #include #include -#include #include #include #include @@ -72,6 +71,7 @@ #include #include #include +#include // preprocessing and filtering #include @@ -2163,119 +2163,7 @@ score += ah.mass_error_p * 1.15386068 + 3.0 * ah.total_MIC + ah.ladder_score; */ - -/* - return - 47.29 * ah.total_loss_score - + 16.93 * ah.partial_loss_score - + 69.35 * ah.mass_error_p - - 72.84 * ah.err - - 75.65 * ah.pl_err - + 26.34 * ah.total_MIC - + 21.85 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) - + 39.64 * ah.ladder_score - + 60.15 * (ah.tag_shifted >= 1); -*/ -/* - return - 64.4 * ah.total_loss_score - + 21.3 * ah.partial_loss_score - + 98.97 * ah.mass_error_p - - 57.57 * ah.err - - 19.23 * ah.pl_err - + 0.23 * ah.total_MIC - + 16.47 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) - + 20.26 * ah.ladder_score - + 4.25 * (ah.tag_shifted >= 1); -*/ -/* - return - 0.90 * ah.total_loss_score - + 0.12 * ah.partial_loss_score - + 2.19 * ah.mass_error_p - - 54.60 * ah.err - - 71.06 * ah.pl_err - + 67.47 * ah.total_MIC - + 66.27 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) - + 11.45 * ah.ladder_score - + 28.09 * (ah.tag_shifted >= 1); -*/ - return ah.modds + ah.pl_modds; - //return sqrt(ah.pl_modds*ah.pl_modds + ah.modds*ah.modds); -/* - const double ret = 1.0 * ah.total_loss_score - + 0.5 * ah.partial_loss_score - + 1.0 * ah.mass_error_p - - 0.001 * ah.err - - 0.001 * ah.pl_err - + isXL * 0.1 * ah.marker_ions_score - + 1.0 * ah.total_MIC - + isXL * (ah.pl_pc_MIC + ah.precursor_score) -// + 1.0 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) - + 0.1 * ah.ladder_score - + 1.0 * (ah.tag_shifted >= 1); - return ret; -*/ - -/* - * [96.45142397 49.37352197 2.61098131 -1.21298196 -4.09934265 28.64381592 - * 53.84125899 41.37187898 7.66281392] - */ - - -/* - * good on IN VITRO: - 1.0 * ah.total_loss_score - + 0.5 * ah.partial_loss_score - + 1.0 * ah.mass_error_p - - 0.1 * ah.err - - 0.1 * ah.pl_err - + isXL * 0.1 * ah.marker_ions_score - + 1.0 * ah.total_MIC - + 1.0 * (ah.pl_pc_MIC > 0 || ah.precursor_score > 0) - + 0.1 * ah.ladder_score - + 1.0 * (ah.tag_shifted >= 1); -*/ -/* - -10.9457 + 1.1836 * isXL + 1.6076 * ah.mass_error_p - 579.912 * ah.err - + 52.2888 * ah.pl_err - 0.0105 * ah.modds - + 88.7997 * ah.immonium_score- 0.88823 * ah.partial_loss_score + 14.2052 * ah.pl_MIC - + 0.61144 * ah.pl_modds + 10.07574543 * ah.pl_pc_MIC -28.05701 * ah.pl_im_MIC - + 2.59655 * ah.total_MIC + 2.38320 * ah.ladder_score + 0.65422535 * (ah.total_loss_score + ah.partial_loss_score) - 4267 without perc / 5306 with perc auf 1- - 5010 with perc auf 2- -*/ - -/* - return - (ah.MIC - 0.00693372) * 0.00317232 - + (ah.Morph - 2.00693) * -5.67908 - + (ah.err - 1.8356e-05) * 0.0074405 - + (ah.immonium_score) * 3.87159 - + (isXL) * -2.8901 - + (ah.ladder_score - 0.0381864) * 2.09632 - + (ah.marker_ions_score) * 2.53656 - + (ah.mass_error_p - 0.6439) * 0.189849 - + (ah.modds - 3.37613e-07) * 9.42353 - + (ah.partial_loss_score) * 4.22367 - + (ah.pl_MIC) * 0.0770935 - + (ah.pl_Morph) * -4.25703 - + (ah.pl_err - 0.000214374) * -0.059863 - + (ah.pl_im_MIC) * -0.367491 - + (ah.pl_modds) * 2.29632 - + (ah.pl_pc_MIC) * 1.13888 - + (ah.precursor_score) * -0.597915 - + (ah.rank_product - 1) * 0.460718 - + (ah.sequence_score - 0.0218818) * -4.68762 - + (ah.tag_XLed) * 2.61103 - + (ah.tag_shifted) * -0.10144 - + (ah.tag_unshifted - 1) * 10.8324 - + (ah.total_MIC - 0.0100453) * 0.836277 - + (ah.total_loss_score - 0.106861) * 34.8899 - + (ah.wTop50 - 2) * -0.248061 - + (ah.sequence.size() - 6) * 0.00656285; // length -*/ } @@ -4593,6 +4481,39 @@ static void scoreXLIons_( if (filtered_spectra > 0) OPENMS_LOG_INFO << " On average " << filtered_peaks_count / (double)filtered_spectra << " peaks per MS2." << endl; } + void addAugmentedFeatures_(vector& pep_ids, const vector& positive_weights) + { + // only for XLs? because they are fewer? + if (pep_ids.empty()) return; + if (pep_ids[0].getHits().empty()) return; + vector keys; + auto p_template = pep_ids[0].getHits()[0]; + p_template.setScore(0); + p_template.getKeys(keys); + + // clear scores + for (const auto& k : keys) + { + if (p_template.getMetaValue(k).valueType() == DataValue::INT_VALUE) p_template.setMetaValue(k, 0); + if (p_template.getMetaValue(k).valueType() == DataValue::DOUBLE_VALUE) p_template.setMetaValue(k, 0.0); + } + + size_t c = 0; + for (const auto& s : positive_weights) + { + auto p = p_template; + p.setMetaValue(s, 1e7); + vector phs; + phs.push_back(p); + PeptideIdentification pid = pep_ids[0]; + pid.setRT(1e6 + c); + pid.setHits(phs); + pep_ids.push_back(pid); + ++c; + } + + } + ExitCodes main_(int, const char**) override { ProgressLogger progresslogger; @@ -4708,7 +4629,7 @@ static void scoreXLIons_( << "-score_type" << "q-value" << "-post_processing_tdc" << "-weights" << weights_out.toQString() - << "-nested_xval_bins" << "3" +// << "-nested_xval_bins" << "3" ; if (getStringOption_("peptide:enzyme") == "Lys-C") @@ -5245,13 +5166,9 @@ static void scoreXLIons_( { if (aas.size() <= 2) { e.sequence += aas.toUnmodifiedString(); continue; } - //cout << "Seq. before reverse: " << s << endl; - //auto last = --s.end(); - //std::reverse(s.begin(), last); // standard peptide reverse - //cout << "Seq. after reverse : " << s << endl; - - // switch cleavage sites (like in Andromeda or DecoyPyrate) - // if (s.size() >= 2) std::swap(s[s.size() - 1], s[s.size() - 2]); + // static const DecoyGenerator dg; + // e.sequence += dg.reversePeptides(aas, enzyme).toUnmodifiedString(); + DecoyGenerator dg; // important to create inside the loop with same seed. Otherwise same peptides end up creating different decoys -> much more decoys than targets dg.setSeed(4711); e.sequence += dg.shufflePeptides(aas, enzyme).toUnmodifiedString(); @@ -6224,6 +6141,31 @@ static void scoreXLIons_( xl_pi.clear(); pep_pi.clear(); */ + vector positive_weights_features = { "NuXL:mass_error_p", "NuXL:total_loss_score", "NuXL:modds", "NuXL:immonium_score", "NuXL:MIC", "NuXL:Morph", "NuXL:total_MIC", "NuXL:ladder_score", "NuXL:sequence_score", + "NuXL:total_Morph", "NuXL:total_HS", "NuXL:tag_XLed", "NuXL:tag_unshifted", "NuXL:tag_shifted", "NuXL:explained_peak_fraction", "NuXL:theo_peak_fraction", + "NuXL:marker_ions_score", "NuXL:partial_loss_score", "NuXL:pl_MIC", "NuXL:pl_Morph", "NuXL:pl_modds", "NuXL:pl_pc_MIC", "NuXL:pl_im_MIC", "NuXL:score" }; +/* + << "NuXL:err" + << "NuXL:immonium_score" + << "NuXL:precursor_score" + << "NuXL:aminoacid_max_tag" + << "NuXL:aminoacid_id_to_max_tag_ratio" + << "nr_candidates" + << "NuXL:wTop50" + + << "NuXL:isPhospho" + << "NuXL:isXL" + << "NuXL:score" + << "isotope_error" + << "variable_modifications" + << "precursor_intensity_log10" + << "NuXL:NA_MASS_z0" + << "NuXL:NA_length" + << "nucleotide_mass_tags" + << "n_theoretical_peaks"; +*/ + // addAugmentedFeatures_(peptide_ids, positive_weights_features); TODO: seems to work ... scales weights but no improvement + // write ProteinIdentifications and PeptideIdentifications to IdXML IdXMLFile().store(out_idxml, protein_ids, peptide_ids); @@ -6281,7 +6223,7 @@ static void scoreXLIons_( << "-score_type" << "svm" << "-unitnorm" << "-post_processing_tdc" - << "-nested_xval_bins" << "3" +// << "-nested_xval_bins" << "3" << "-weights" << weights_out.toQString() << "-out_pin" << pin.toQString(); From 51d10469f2f6ab810eddc4da9b1cb1fb7c1beea6 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 8 Sep 2021 12:15:08 +0200 Subject: [PATCH 189/471] moved mod generator --- .../ANALYSIS/ID/SimpleSearchEngineAlgorithm.h | 2 +- .../OpenMS/ANALYSIS/NUXL/NuXLAnnotateAndLocate.h | 2 +- .../include/OpenMS/ANALYSIS/NUXL/NuXLConstants.h | 2 +- .../include/OpenMS/ANALYSIS/XLMS/OPXLHelper.h | 2 +- src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp | 2 +- src/utils/MetaProSIP.cpp | 13 +++++++++++-- 6 files changed, 16 insertions(+), 7 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h b/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h index 1c589e55760..324d56a94e2 100644 --- a/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h +++ b/src/openms/include/OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h @@ -35,7 +35,7 @@ #include #include -#include +#include #include #include diff --git a/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLAnnotateAndLocate.h b/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLAnnotateAndLocate.h index 4945d63e12c..84d11429f7d 100644 --- a/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLAnnotateAndLocate.h +++ b/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLAnnotateAndLocate.h @@ -36,7 +36,7 @@ #include #include -#include +#include #include #include diff --git a/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLConstants.h b/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLConstants.h index d907bb381c8..28198bb818e 100644 --- a/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLConstants.h +++ b/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLConstants.h @@ -36,7 +36,7 @@ #include #include -#include +#include #include #include diff --git a/src/openms/include/OpenMS/ANALYSIS/XLMS/OPXLHelper.h b/src/openms/include/OpenMS/ANALYSIS/XLMS/OPXLHelper.h index caf5d1d815b..29a66f66680 100644 --- a/src/openms/include/OpenMS/ANALYSIS/XLMS/OPXLHelper.h +++ b/src/openms/include/OpenMS/ANALYSIS/XLMS/OPXLHelper.h @@ -39,7 +39,7 @@ #include #include #include -#include +#include #include namespace OpenMS diff --git a/src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp b/src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp index 33d0ea00cf2..182d52767a9 100644 --- a/src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp +++ b/src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp @@ -33,7 +33,7 @@ // -------------------------------------------------------------------------- #include -#include +#include #include #include #include diff --git a/src/utils/MetaProSIP.cpp b/src/utils/MetaProSIP.cpp index beb14d9165f..751c393593b 100644 --- a/src/utils/MetaProSIP.cpp +++ b/src/utils/MetaProSIP.cpp @@ -1378,7 +1378,7 @@ class MetaProSIPDecomposition if (modifications_ef.getNumberOf(e1) > 0) // modification adds additional (unlabeled) carbon atoms { IsotopeDistribution modification_dist = modifications_ef.getIsotopeDistribution(CoarseIsotopePatternGenerator(max_labeling_carbon + additional_isotopes)); - + for (double abundance = 0.0; abundance < 100.0 - 1e-8; abundance += 100.0 / (double)max_labeling_carbon) { double a = abundance / 100.0; @@ -1389,6 +1389,7 @@ class MetaProSIPDecomposition e2->setIsotopeDistribution(isotopes); IsotopeDistribution dist = unmodified_peptide_ef.getIsotopeDistribution(CoarseIsotopePatternGenerator(max_labeling_carbon + additional_isotopes)); dist.set(CoarseIsotopePatternGenerator().convolve_(dist.getContainer(), modification_dist.getContainer())); // convolve with modification distribution (which follows the natural distribution) + // size is now modification_dist.size() + dist.size() IsotopeDistribution::ContainerType container = dist.getContainer(); vector intensities; for (Size i = 0; i != container.size(); ++i) @@ -1926,10 +1927,13 @@ class MetaProSIPXICExtraction xic_mzs.push_back(mz); } + cout << "Element count (+ additional isotopes): " << element_count << endl; + // extract xics vector > xics = extractXICs(seed_rt, xic_mzs, mz_tolerance_ppm, rt_tolerance_s, peak_map); vector xic_intensities(xics.size(), 0.0); + if (min_corr_mono > 0) { // calculate correlation to mono-isotopic peak @@ -1950,6 +1954,8 @@ class MetaProSIPXICExtraction } } + cout << "XICs: " << xic_intensities.size() << endl; + return xic_intensities; } @@ -2139,7 +2145,7 @@ class RIntegration { if (std::distance(pattern_begin, pattern_end) != std::distance(intensities_begin, intensities_end)) { - OPENMS_LOG_ERROR << "Error: size of pattern and collected intensities don't match!: (pattern " << std::distance(pattern_begin, pattern_end) << ") (intensities " << std::distance(intensities_begin, intensities_end) << ")" << endl; + cout << "Error: size of pattern and collected intensities don't match!: (pattern " << std::distance(pattern_begin, pattern_end) << ") (intensities " << std::distance(intensities_begin, intensities_end) << ")" << endl; } if (pattern_begin == pattern_end) @@ -3292,9 +3298,11 @@ class RIntegration if (sip_peptide.feature_type == FEATURE_STRING || sip_peptide.feature_type == UNASSIGNED_ID_STRING) { element_count = MetaProSIPDecomposition::getNumberOfLabelingElements(labeling_element, feature_hit_aaseq); + cout << "Numver of labeling elements: " << element_count << "\t" << feature_hit_aaseq.toString() << endl; } else // if (sip_peptide.feature_type == UNIDENTIFIED_STRING) { + cout << "Unidentified" << endl; // calculate number of expected labeling elements using averagine model C:4.9384 H:7.7583 N:1.3577 O:1.4773 S:0.0417 divided by average weight 111.1254 if (labeling_element == "C") { @@ -3449,6 +3457,7 @@ class RIntegration sip_peptide.patterns = patterns; for (IsotopePatterns::const_iterator pit = sip_peptide.patterns.begin(); pit != sip_peptide.patterns.end(); ++pit) { + cout << pit->first << "\t" << pit->second.size() << endl; PeakSpectrum p = isotopicIntensitiesToSpectrum(feature_hit_theoretical_mz, sip_peptide.mass_diff, feature_hit_charge, pit->second); p.setMetaValue("rate", (double)pit->first); p.setMSLevel(2); From d6c793a1a54aaf832f608c53717ccdd1b689f182 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 2 Nov 2021 10:06:36 +0100 Subject: [PATCH 190/471] removed old C11 code --- src/utils/OpenNuXL.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 511d2d8cba7..888e16830c2 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -6392,7 +6392,7 @@ map OpenNuXL::mass2high_frequency_ = {}; #endif map>> OpenNuXL::fragment_adduct2block_if_masses_present = {}; - +/* constexpr std::array OpenNuXL::modifications_RNA_UV; // TODO: remove with C17 see https://stackoverflow.com/questions/8016780/undefined-reference-to-static-constexpr-char constexpr std::array OpenNuXL::fragments_RNA_UV; constexpr std::array OpenNuXL::modifications_RNA_UV_4SU; @@ -6411,7 +6411,7 @@ constexpr std::array OpenNuXL::DNA_nucleotides; constexpr std::array OpenNuXL::RNA_nucleotides; constexpr std::array OpenNuXL::DNA_mapping; constexpr std::array OpenNuXL::RNA_mapping; - +*/ int main(int argc, const char** argv) { OpenNuXL tool; From 0d22340d9bdefa7e8a070cee5ecad48b3b4e733e Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Tue, 2 Nov 2021 16:05:31 +0100 Subject: [PATCH 191/471] first update of presets, disabled fragment frequency scaling --- src/utils/OpenNuXL.cpp | 671 ++++++++++++++++++++++++++++++++++++----- 1 file changed, 591 insertions(+), 80 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 888e16830c2..b26fb3d9cdd 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -263,29 +263,35 @@ class OpenNuXL : static constexpr double MIN_TOTAL_LOSS_IONS = 1; // minimum number of matches to unshifted ions static constexpr double MIN_SHIFTED_IONS = 1; // minimum number of matches to shifted ions (applies to XLs only) - static constexpr std::array modifications_RNA_UV + static constexpr std::array modifications_RNA_UV_PASE {"U:", "U:-H2O", - "U:-H2O-HPO3", - "U:-HPO3", + "U:-H3PO4", + "U:-HPO3", + "C:", "C:-NH3", "C:-H2O", "C:-NH3-HPO3", - "C:-H2O-HPO3", - "C:-HPO3", + "C:-H3PO4", + "C:-HPO3", + "G:", "G:-H2O", "G:-NH3", - "G:-H2O-HPO3", + "G:-H3PO4", "G:-NH3-HPO3", - "G:-HPO3", + "G:-HPO3", + "A:", + "A:-H2O", + "A:-HPO3" + "A:-H3PO4", "A:-NH3", - "A:-NH3-HPO3", - "A:-HPO3"}; + "A:-NH3-HPO3" + }; - static constexpr std::array fragments_RNA_UV + static constexpr std::array fragments_RNA_UV_PASE {"U:C9H10N2O5;U-H3PO4", "U:C4H4N2O2;U'", "U:C4H2N2O1;U'-H2O", @@ -293,17 +299,71 @@ class OpenNuXL : "U:C9H13N2O9P1;U", "U:C9H11N2O8P1;U-H2O", "U:C9H12N2O6;U-HPO3", - "U:C5H9O7P;ribose", - "U:C5H7O6P;ribose-H2O", - "U:C5H6O3;ribose-H2O-HPO3", + "C:C9H14N3O8P;C", "C:C9H11N2O8P;C-NH3", "C:C9H12N3O7P;C-H2O", "C:C9H13N3O5;C-HPO3", "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", "C:C4H5N3O;C'", "C:C4H3N3;C'-H2O", "C:C4H2N2O;C'-NH3", + + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H13N5O5;G-HPO3", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3" + }; + static constexpr std::array modifications_RNA_UV + {"U:", + "U:-H2O", + + "C:", + "C:-NH3", + "C:-H2O", + + "G:", + "G:-H2O", + "G:-NH3", + + "A:", + "A:-H2O", + "A:-NH3" + }; + + static constexpr std::array fragments_RNA_UV + {"U:C9H10N2O5;U-H3PO4", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C3O;C3O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "G:C10H14N5O8P;G", "G:C10H12N5O7P;G-H2O", "G:C10H11N4O8P;G-NH3", @@ -314,6 +374,7 @@ class OpenNuXL : "G:C5H5N5O;G'", "G:C5H3N5;G'-H2O", "G:C5H2N4O;G'-NH3", + "A:C10H14N5O7P;A", "A:C10H12N5O6P;A-H2O", "A:C10H11N4O7P;A-NH3", @@ -321,18 +382,11 @@ class OpenNuXL : "A:C10H11N5O3;A-H3PO4", "A:C10H10N5O4;A-NH3-HPO3", "A:C5H5N5;A'", - "A:C5H2N4;A'-NH3", - "C:C5H9O7P;ribose", - "G:C5H9O7P;ribose", - "A:C5H9O7P;ribose", - "G:C5H7O6P;rib-H2O", - "C:C5H7O6P;rib-H2O", - "A:C5H7O6P;rib-H2O", - "G:C5H6O3;ribose-H2O-HPO3", - "C:C5H6O3;ribose-H2O-HPO3", - "A:C5H6O3;ribose-H2O-HPO3"}; + "A:C5H2N4;A'-NH3" + }; - static constexpr std::array modifications_RNA_UV_4SU + + static constexpr std::array modifications_RNA_UV_4SU_PASE { "S:", "S:-H2O", "S:-H2O-HPO3", @@ -341,8 +395,9 @@ class OpenNuXL : "S:-H2S" }; - static constexpr std::array fragments_RNA_UV_4SU + static constexpr std::array fragments_RNA_UV_4SU_PASE { "S:C4H2N2O1;tU-H2S", + "U:C9H10N2O5;U-H3PO4", "U:C4H4N2O2;U'", "U:C4H2N2O1;U'-H2O", @@ -350,9 +405,7 @@ class OpenNuXL : "U:C9H13N2O9P1;U", "U:C9H11N2O8P1;U-H2O", "U:C9H12N2O6;U-HPO3", - "U:C5H9O7P;ribose", - "U:C5H7O6P;ribose-H2O", - "U:C5H6O3;ribose-H2O-HPO3", + "C:C9H14N3O8P;C", "C:C9H11N2O8P;C-NH3", "C:C9H12N3O7P;C-H2O", @@ -361,6 +414,7 @@ class OpenNuXL : "C:C4H5N3O;C'", "C:C4H3N3;C'-H2O", "C:C4H2N2O;C'-NH3", + "G:C10H14N5O8P;G", "G:C10H12N5O7P;G-H2O", "G:C10H11N4O8P;G-NH3", @@ -371,6 +425,7 @@ class OpenNuXL : "G:C5H5N5O;G'", "G:C5H3N5;G'-H2O", "G:C5H2N4O;G'-NH3", + "A:C10H14N5O7P;A", "A:C10H12N5O6P;A-H2O", "A:C10H11N4O7P;A-NH3", @@ -378,64 +433,179 @@ class OpenNuXL : "A:C10H11N5O3;A-H3PO4", "A:C10H10N5O4;A-NH3-HPO3", "A:C5H5N5;A'", - "A:C5H2N4;A'-NH3", - "C:C5H9O7P;ribose", - "G:C5H9O7P;ribose", - "A:C5H9O7P;ribose", - "G:C5H7O6P;rib-H2O", - "C:C5H7O6P;rib-H2O", - "A:C5H7O6P;rib-H2O", - "G:C5H6O3;ribose-H2O-HPO3", - "C:C5H6O3;ribose-H2O-HPO3", - "A:C5H6O3;ribose-H2O-HPO3" + "A:C5H2N4;A'-NH3" }; - static constexpr std::array modifications_DNA_UV + static constexpr std::array modifications_RNA_UV_4SU + { "S:", + "S:-H2O", + "S:-H2S+HPO3", + "S:-H2S" + }; + + static constexpr std::array fragments_RNA_UV_4SU + { "S:C4H2N2O1;tU-H2S", + + "U:C9H10N2O5;U-H3PO4", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C3O;C3O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H13N5O5;G-HPO3", + "C:C9H10N2O5;C-NH3-HPO3", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3" + }; + + + static constexpr std::array modifications_DNA_UV + {"T:", + "T:-H2O", + "T:+C5H7O5P", // + dribose-H2O + "T:-C5H6N2O2", + + "G:", + "G:-H2O", + "G:-NH3", + "G:+C5H7O5P", + "G:-C5H5N5O", + + "A:-NH3", + "A:+C5H7O5P", + "A:", + "A:-H2O", + "A:-C5H5N5", + + "C:", + "C:-H2O", + "C:-NH3", + "C:+C5H7O5P", + "C:-C4H5N3O" // loss of base -> only dribose remains + }; + + static constexpr std::array fragments_DNA_UV + {"T:C10H15N2O8P;T", + "T:C10H13N2O7P;T-H2O", + "T:C10H14N2O5;T-HPO3", + "T:C10H12N2O4;T-H3PO4", + "T:C5H6N2O2;T'", + "T:C5H4N2O;T'-H2O", + + "C:C9H14N3O7P;C", + "C:C9H11N2O7P;C-NH3", + "C:C9H12N3O6P;C-H2O", + "C:C9H13N3O4;C-HPO3", + "C:C9H11N3O3;C-H3PO4", + "C:C9H10N2O4;C-NH3-HPO3", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + + "G:C10H14N5O7P;G", + "G:C10H12N5O6P;G-H2O", + "G:C10H11N4O7P;G-NH3", + "G:C10H13N5O4;G-HPO3", + "G:C10H10N4O4;G-NH3-HPO3", + "G:C10H11N5O3;G-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + + "A:C10H14N5O6P;A", + "A:C10H12N5O5P;A-H2O", + "A:C10H11N4O6P;A-NH3", + "A:C10H13N5O3;A-HPO3", + "A:C10H11N5O2;A-H3PO4", + "A:C10H10N5O3;A-NH3-HPO3", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + + "A:C5H9O6P;C5H9O6P", // base was lost -> only dribose = C5H9O6P remains + "G:C5H9O6P;C5H9O6P", + "C:C5H9O6P;C5H9O6P", + "T:C5H9O6P;C5H9O6P", + "A:C5H7O5P;C5H9O6P-H2O", + "G:C5H7O5P;C5H9O6P-H2O", + "C:C5H7O5P;C5H9O6P-H2O", + "T:C5H7O5P;C5H9O6P-H2O", + "A:C5H8O3;C5H9O6P-HPO3", + "G:C5H8O3;C5H9O6P-HPO3", + "C:C5H8O3;C5H9O6P-HPO3", + "T:C5H8O3;C5H9O6P-HPO3" + }; + + static constexpr std::array modifications_DNA_UV_PASE {"T:", "T:-H2O", "T:-H2O-HPO3", "T:-HPO3", + "A:", "A:-H2O", "A:-H2O-HPO3", "A:-HPO3", + "A:-NH3", + "G:", "G:-H2O", "G:-NH3", - "A:-NH3", "G:-HPO3", "G:-H2O-HPO3", "G:-NH3-HPO3", + "C:", "C:-H2O", "C:-NH3", "C:-H2O-HPO3", "C:-NH3", "C:-NH3-HPO3", + "T:+C5H7O5P", // + dribose-H2O "A:+C5H7O5P", "G:+C5H7O5P", "C:+C5H7O5P", + "C:-C4H5N3O", // loss of base -> only dribose remains "T:-C5H6N2O2", "G:-C5H5N5O", - "A:-C5H5N5", - "T:+HPO3", - "C:+HPO3", - "A:+HPO3", - "G:+HPO3", - "T:+HPO3-H2O", - "C:+HPO3-H2O", - "A:+HPO3-H2O", - "G:+HPO3-H2O"}; + "A:-C5H5N5" + }; - static constexpr std::array fragments_DNA_UV + static constexpr std::array fragments_DNA_UV_PASE {"T:C10H15N2O8P;T", "T:C10H13N2O7P;T-H2O", "T:C10H14N2O5;T-HPO3", "T:C10H12N2O4;T-H3PO4", "T:C5H6N2O2;T'", "T:C5H4N2O;T'-H2O", + "C:C9H14N3O7P;C", "C:C9H11N2O7P;C-NH3", "C:C9H12N3O6P;C-H2O", @@ -445,6 +615,7 @@ class OpenNuXL : "C:C4H5N3O;C'", "C:C4H3N3;C'-H2O", "C:C4H2N2O;C'-NH3", + "G:C10H14N5O7P;G", "G:C10H12N5O6P;G-H2O", "G:C10H11N4O7P;G-NH3", @@ -454,6 +625,7 @@ class OpenNuXL : "G:C5H5N5O;G'", "G:C5H3N5;G'-H2O", "G:C5H2N4O;G'-NH3", + "A:C10H14N5O6P;A", "A:C10H12N5O5P;A-H2O", "A:C10H11N4O6P;A-NH3", @@ -462,27 +634,29 @@ class OpenNuXL : "A:C10H10N5O3;A-NH3-HPO3", "A:C5H5N5;A'", "A:C5H2N4;A'-NH3", - "A:C5H9O6P;dribose", // base was lost -> only dribose remains - "G:C5H9O6P;dribose", - "C:C5H9O6P;dribose", - "T:C5H9O6P;dribose", - "A:C5H7O5P;dribose-H2O", - "G:C5H7O5P;dribose-H2O", - "C:C5H7O5P;dribose-H2O", - "T:C5H7O5P;dribose-H2O", - "A:C5H8O3;dribose-HPO3", - "G:C5H8O3;dribose-HPO3", - "C:C5H8O3;dribose-HPO3", - "T:C5H8O3;dribose-HPO3" + + "A:C5H9O6P;C5H9O6P", // base was lost -> only dribose = C5H9O6P remains + "G:C5H9O6P;C5H9O6P", + "C:C5H9O6P;C5H9O6P", + "T:C5H9O6P;C5H9O6P", + "A:C5H7O5P;C5H9O6P-H2O", + "G:C5H7O5P;C5H9O6P-H2O", + "C:C5H7O5P;C5H9O6P-H2O", + "T:C5H7O5P;C5H9O6P-H2O", + "A:C5H8O3;C5H9O6P-HPO3", + "G:C5H8O3;C5H9O6P-HPO3", + "C:C5H8O3;C5H9O6P-HPO3", + "T:C5H8O3;C5H9O6P-HPO3" }; - static constexpr std::array modifications_RNA_DEB + static constexpr std::array modifications_RNA_DEB_PASE { "U:+C4H6O2", "U:+C4H6O2-H2O", "U:+C4H6O2-HPO3", "U:+C4H6O2-H3PO4", "U:+C4H6O2-H2O-H2O", "U:+C4H6O2-H3PO4-H2O", + "G:+C4H6O2", "G:+C4H6O2-H2O", "G:+C4H6O2-HPO3", @@ -490,20 +664,89 @@ class OpenNuXL : "G:+C4H6O2-H2O-H2O", "G:+C4H6O2-H3PO4-H2O", "G:+C4H6O2-NH3", + "G:+C4H602-NH3-HPO3", + "C:+C4H6O2", "C:+C4H6O2-H2O", "C:+C4H6O2-HPO3", "C:+C4H6O2-H3PO4", "C:+C4H6O2-H2O-H2O", "C:+C4H6O2-H3PO4-H2O", - "C:+C4H6O2-H2O", "C:+C4H6O2-NH3", + "C:+C4H602-NH3-HPO3", + "A:+C4H6O2", "A:+C4H6O2-H2O", "A:+C4H6O2-HPO3", "A:+C4H6O2-H3PO4", "A:+C4H6O2-H2O-H2O", "A:+C4H6O2-H3PO4-H2O", + "A:+C4H6O2-NH3", + "A:+C4H602-NH3-HPO3" + }; + + static constexpr std::array fragments_RNA_DEB_PASE + { + "U:C4H6O2;DEB", + "U:C4H4O;DEB-H2O", + "U:C13H16N2O7;DEB+U-H3PO4", + "U:C8H10N2O4;DEB+U'", + "U:C8H8N2O3;DEB+U'-H2O", + "U:C7H6O3;DEB+C3O", + "U:C13H19N2O11P1;DEB+U", + "U:C13H17N2O10P1;DEB+U-H2O", + "U:C13H16N2O7;DEB+U-H3PO4", + + "G:C4H6O2;DEB", + "G:C4H4O;DEB-H2O", + "G:C14H17N5O6;DEB+G-H3PO4", + "G:C9H11N5O3;DEB+G'", + "G:C8H9N5O3;DEB+G'-H2O", + "G:C14H20N5O10P1;DEB+G", + "G:C14H18N5O9P1;DEB+G-H2O", + "G:C14H17N5O6;DEB+G-H3PO4", + + "C:C4H6O2;DEB", + "C:C4H4O;DEB-H2O", + "C:C13H17N3O6;DEB+C-H3PO4", + "C:C8H11N3O3;DEB+C'", + "C:C8H9N3O2;DEB+C'-H2O", + "C:C13H20N3O10P1;DEB+C", + "C:C13H18N3O9P1;DEB+C-H2O", + "C:C13H17N3O6;DEB+C-H3PO4", + + "A:C4H6O2;DEB", + "A:C4H4O;DEB-H2O", + "A:C14H17N5O5;DEB+A-H3PO4", + "A:C9H11N5O2;DEB+A'", + "A:C8H9N5O2;DEB+A'-H2O", + "A:C14H20N5O9P1;DEB+A", + "A:C14H18N5O8P1;DEB+A-H2O", + "A:C14H17N5O5;DEB+A-H3PO4", + "A:C19H12N5O6P;A-H2O", + "A:C9H17N4O;DEB+A'-NH3", + "A:C14H17N4O9;DEB+A-NH3" + }; + + static constexpr std::array modifications_RNA_DEB + { "U:+C4H6O2", + "U:+C4H6O2-H2O", + "U:+C4H6O2-H2O-H2O", + + "G:+C4H6O2", + "G:+C4H6O2-H2O", + "G:+C4H6O2-H2O-H2O", + "G:+C4H6O2-NH3", + + "C:+C4H6O2", + "C:+C4H6O2-H2O", + "C:+C4H6O2-H2O-H2O", + "C:+C4H6O2-H2O", + "C:+C4H6O2-NH3", + + "A:+C4H6O2", + "A:+C4H6O2-H2O", + "A:+C4H6O2-H2O-H2O", "A:+C4H6O2-H2O", "A:+C4H6O2-NH3" }; @@ -519,6 +762,7 @@ class OpenNuXL : "U:C13H19N2O11P1;DEB+U", "U:C13H17N2O10P1;DEB+U-H2O", "U:C13H16N2O7;DEB+U-H3PO4", + "G:C4H6O2;DEB", "G:C4H4O;DEB-H2O", "G:C14H17N5O6;DEB+G-H3PO4", @@ -527,6 +771,7 @@ class OpenNuXL : "G:C14H20N5O10P1;DEB+G", "G:C14H18N5O9P1;DEB+G-H2O", "G:C14H17N5O6;DEB+G-H3PO4", + "C:C4H6O2;DEB", "C:C4H4O;DEB-H2O", "C:C13H17N3O6;DEB+C-H3PO4", @@ -535,6 +780,7 @@ class OpenNuXL : "C:C13H20N3O10P1;DEB+C", "C:C13H18N3O9P1;DEB+C-H2O", "C:C13H17N3O6;DEB+C-H3PO4", + "A:C4H6O2;DEB", "A:C4H4O;DEB-H2O", "A:C14H17N5O5;DEB+A-H3PO4", @@ -548,18 +794,26 @@ class OpenNuXL : "A:C14H17N4O9;DEB+A-NH3" }; - static constexpr std::array modifications_DNA_DEB + static constexpr std::array modifications_DNA_DEB { // adapted from Fanni + water losses "T:+C4H6O2", "T:+C4H6O2-H2O", + "T:+C4H6O2-H2O-H2O", + "G:+C4H6O2", - "G:+C4H6O2-C5H9O6P", - "G:+C4H6O2-H2O-C5H9O6P", "G:+C4H6O2-H2O", + "G:+C4H6O2-H2O-H2O", + "G:+C4H6O2-NH3", + "C:+C4H6O2", "C:+C4H6O2-H2O", + "C:+C4H6O2-H2O-H2O", + "C:+C4H6O2-NH3", + "A:+C4H6O2", "A:+C4H6O2-H2O" + "A:+C4H6O2-H2O-H2O", + "A:+C4H6O2-NH3" }; static constexpr std::array fragments_DNA_DEB @@ -572,6 +826,7 @@ class OpenNuXL : "T:C14H19N2O9P1;DEB+T-H2O", "T:C14H20N2O7;DEB+T-HPO3", // C4H6O2 + C10H15N2O8P - HPO3 "T:C14H18N2O6;DEB+T-H3PO4", // C4H6O2 + C10H15N2O8P - H3PO4 + "C:C4H6O2;DEB", "C:C4H4O;DEB-H2O", "C:C4H5N3O;C'", // needed for marker ion @@ -583,6 +838,7 @@ class OpenNuXL : "C:C13H18N3O8P1;DEB+C-H2O", // "C:C13H19N3O6;DEB+C-HPO3", // "C:C13H17N3O5;DEB+C-H3PO4", + "G:C4H6O2;DEB", "G:C4H4O;DEB-H2O", "G:C9H11N5O3;DEB+G'", @@ -593,6 +849,7 @@ class OpenNuXL : "G:C14H18N5O8P1;DEB+G-H2O", // not in Fanni's list // "G:C14H19N5O6;DEB+G-HPO3", // "G:C14H17N5O5;DEB+G-H3PO4", + "A:C4H6O2;DEB", "A:C4H4O;DEB-H2O", "A:C5H5N5;A'", // needed for marker ion @@ -607,20 +864,103 @@ class OpenNuXL : // "A:C14H17N5O4;DEB+A-H3PO4" // C4H6O2 + C10H14N5O6P - H3PO4 }; - static constexpr std::array modifications_RNA_NM + static constexpr std::array modifications_DNA_DEB_PASE + // adapted from Fanni + water losses + {"T:+C4H6O2", + "T:+C4H6O2-HPO3", + "T:+C4H6O2-H3PO4", + "T:+C4H6O2-H2O-H2O", + "T:+C4H6O2-H3PO4-H2O", + "T:+C4H6O2-H2O", + + "G:+C4H6O2", + "G:+C4H6O2-HPO3", + "G:+C4H6O2-H3PO4", + "G:+C4H6O2-H2O-H2O", + "G:+C4H6O2-H3PO4-H2O", + "G:+C4H6O2-H2O", + "G:+C4H6O2-NH3", + "G:+C4H6O2-NH3-HPO3", + + "C:+C4H6O2", + "C:+C4H6O2-H2O", + "C:+C4H6O2-HPO3", + "C:+C4H6O2-H3PO4", + "C:+C4H6O2-H2O-H2O", + "C:+C4H6O2-H3PO4-H2O", + "C:+C4H6O2-NH3", + "C:+C4H6O2-NH3-HPO3", + + "A:+C4H6O2", + "A:+C4H6O2-H2O", + "A:+C4H6O2-H3PO4-H2O", + "A:+C4H6O2-H2O-H2O", + "A:+C4H6O2-H3PO4", + "A:+C4H6O2-HPO3", + "A:+C4H6O2-NH3", + "A:+C4H6O2-NH3-HPO3" + }; + + static constexpr std::array fragments_DNA_DEB_PASE + { "T:C4H6O2;DEB", + "T:C4H4O;DEB-H2O", + "T:C5H6N2O2;T'", // needed for marker ion + "T:C9H12N2O4;DEB+T'", + "T:C9H10N2O3;DEB+T'-H2O", + "T:C14H21N2O10P1;DEB+T", // C4H6O2 + C10H15N2O8P + "T:C14H19N2O9P1;DEB+T-H2O", + "T:C14H20N2O7;DEB+T-HPO3", // C4H6O2 + C10H15N2O8P - HPO3 + "T:C14H18N2O6;DEB+T-H3PO4", // C4H6O2 + C10H15N2O8P - H3PO4 + "C:C4H6O2;DEB", + "C:C4H4O;DEB-H2O", + "C:C4H5N3O;C'", // needed for marker ion + "C:C8H11N3O3;DEB+C'", + "C:C8H8N2O3;DEB+C'-NH3", + "C:C8H9N3O2;DEB+C'-H2O", + "C:C13H20N3O9P1;DEB+C", + "C:C13H17N2O9P1;DEB+C-NH3", + "C:C13H18N3O8P1;DEB+C-H2O", +// "C:C13H19N3O6;DEB+C-HPO3", +// "C:C13H17N3O5;DEB+C-H3PO4", + "G:C4H6O2;DEB", + "G:C4H4O;DEB-H2O", + "G:C9H11N5O3;DEB+G'", + "G:C9H9N5O2;DEB+G'-H2O", + "G:C14H20N5O9P1;DEB+G", + "G:C5H5N5O;G'", // needed for marker ion + "G:C10H9N5O2;G-H3PO4-H2O", // exclusive to Fanni + "G:C14H18N5O8P1;DEB+G-H2O", // not in Fanni's list +// "G:C14H19N5O6;DEB+G-HPO3", +// "G:C14H17N5O5;DEB+G-H3PO4", + "A:C4H6O2;DEB", + "A:C4H4O;DEB-H2O", + "A:C5H5N5;A'", // needed for marker ion + "A:C9H11N5O2;DEB+A'", // C4H6O2 + C5H5N5 + "A:C9H9N5O1;DEB+A'-H2O", // not in Fanni's list + "A:C9H8N4O2;DEB+A'-NH3", // C4H6O2 + C5H5N5 - NH3 + "A:C14H20N5O8P1;DEB+A", // C4H6O2 + C10H14N5O6P + "A:C14H17N4O8P1;DEB+A-NH3", // C4H6O2 + C10H14N5O6P - NH3 + "A:C14H18N5O7P1;DEB+A-H2O", // not in Fanni's list + "A:C10H9N5O;A-H3PO4-H2O" // Fanni +// "A:C14H19N5O5;DEB+A-HPO3", // C4H6O2 + C10H14N5O6P - HPO3 +// "A:C14H17N5O4;DEB+A-H3PO4" // C4H6O2 + C10H14N5O6P - H3PO4 + }; + + + static constexpr std::array modifications_RNA_NM_PASE {"U:+C5H9N1", "U:+C5H9N1-HPO3", + "U:+C5H9N1-H2O", "U:+C5H9N1-H3PO4", "U:+C5H9N1-H2O-H2O", "U:+C5H9N1-H3PO4-H2O", - "U:+C5H9N1-H2O", "G:+C5H9N1", "G:+C5H9N1-HPO3", + "G:+C5H9N1-H2O", "G:+C5H9N1-H3PO4", "G:+C5H9N1-H2O-H2O", "G:+C5H9N1-H3PO4-H2O", - "G:+C5H9N1-H2O", "G:+C5H9N1-NH3", "C:+C5H9N1", @@ -640,7 +980,7 @@ class OpenNuXL : "A:+C5H9N1-NH3" }; - static constexpr std::array fragments_RNA_NM + static constexpr std::array fragments_RNA_NM_PASE {"U:C5H9N1;NM", "U:C14H21N3O6;NM+U-HPO3", "U:C9H13N3O2;NM+U'", @@ -649,12 +989,17 @@ class OpenNuXL : "U:C14H22N3O9P1;NM+U", "U:C14H20N3O8P1;NM+U-H2O", "U:C14H19N3O5;NM+U-H3PO4", + "C:C5H9N1;NM", "C:C14H20N4O4;NM+C-H3PO4", "C:C9H14N4O1;NM+C'", "C:C9H12N4;NM+C'-H2O", "C:C14H23N4O8P1;NM+C", "C:C14H21N4O7P1;NM+C-H2O", + "C:C14H22N4O5;NM+C-HPO3", + "C:C14H20N3O8P1;NM+C-NH3", + "C:C9H11N3O1;NM+C'-NH3", + "G:C5H9N1;NM", "G:C15H22N6O5;NM+G-HPO3", "G:C10H14N6O1;NM+G'", @@ -662,35 +1007,157 @@ class OpenNuXL : "G:C15H23N6O8P1;NM+G", "G:C15H21N6O7P1;NM+G-H2O", "G:C15H20N6O4;NM+G-H3PO4", + "G:C10H14N6O1;NM+G'-NH3", + "A:C5H9N1;NM", "A:C10H14N6;NM+A'", "A:C10H11N5;NM+A'-NH3", "A:C15H23N6O7P1;NM+A", "A:C15H20N6O3;NM+A-H3PO4", "A:C15H21N6O6P1;NM+A-H2O", + "A:C15H22N6O4;NM+A-HPO3" + }; + + static constexpr std::array modifications_RNA_NM + {"U:+C5H9N1", + "U:+C5H9N1-H2O-H2O", + "U:+C5H9N1-H2O", + + "G:+C5H9N1", + "G:+C5H9N1-H2O-H2O", + "G:+C5H9N1-H2O", + "G:+C5H9N1-NH3", + + "C:+C5H9N1", + "C:+C5H9N1-H2O", + "C:+C5H9N1-H2O-H2O", + "C:+C5H9N1-NH3", + + "A:+C5H9N1", + "A:+C5H9N1-H2O", + "A:+C5H9N1-H2O-H2O", + "A:+C5H9N1-NH3" + }; + + static constexpr std::array fragments_RNA_NM + {"U:C5H9N1;NM", + "U:C14H21N3O6;NM+U-HPO3", + "U:C9H13N3O2;NM+U'", + "U:C9H11N3O1;NM+U'-H2O", + "U:C8H9N1O1;NM+C3O", + "U:C14H22N3O9P1;NM+U", + "U:C14H20N3O8P1;NM+U-H2O", + "U:C14H19N3O5;NM+U-H3PO4", + + "C:C5H9N1;NM", + "C:C14H20N4O4;NM+C-H3PO4", + "C:C9H14N4O1;NM+C'", + "C:C9H12N4;NM+C'-H2O", + "C:C14H23N4O8P1;NM+C", + "C:C14H21N4O7P1;NM+C-H2O", "C:C14H22N4O5;NM+C-HPO3", "C:C14H20N3O8P1;NM+C-NH3", "C:C9H11N3O1;NM+C'-NH3", + + "G:C5H9N1;NM", + "G:C15H22N6O5;NM+G-HPO3", + "G:C10H14N6O1;NM+G'", + "G:C10H12N6;NM+G'-H2O", + "G:C15H23N6O8P1;NM+G", + "G:C15H21N6O7P1;NM+G-H2O", + "G:C15H20N6O4;NM+G-H3PO4", "G:C10H14N6O1;NM+G'-NH3", + + "A:C5H9N1;NM", + "A:C10H14N6;NM+A'", + "A:C10H11N5;NM+A'-NH3", + "A:C15H23N6O7P1;NM+A", + "A:C15H20N6O3;NM+A-H3PO4", + "A:C15H21N6O6P1;NM+A-H2O", "A:C15H22N6O4;NM+A-HPO3" }; - static constexpr std::array modifications_DNA_NM + + static constexpr std::array modifications_DNA_NM {"T:+C5H9N1", + "T:+C5H9N1-H2O-H2O", + "T:+C5H9N1-H2O", + + "G:+C5H9N1", + "G:+C5H9N1-H2O-H2O", + "G:+C5H9N1-H2O", + "G:+C5H9N1-NH3", + + "C:+C5H9N1", + "C:+C5H9N1-H2O", + "C:+C5H9N1-H2O-H2O", + "C:+C5H9N1-NH3", + + "A:+C5H9N1", + "A:+C5H9N1-H2O", + "A:+C5H9N1-H2O-H2O", + "A:+C5H9N1-NH3", + }; + + static constexpr std::array fragments_DNA_NM + { "T:C5H9N1;NM", + "T:C14H19N3O5;NM+T-H3PO4", + "T:C10H15N3O2;NM+T'", + "T:C10H13N3O1;NM+T'-H2O", + "T:C15H24N3O8P1;NM+T", + "T:C15H22N3O7P1;NM+T-H2O", + "T:C15H19N3O4;NM+T-H3PO4", + "T:C10H12N2O2;NM+T'", + "T:C15H20N2O8P1;NM+T-NH3", + "T:C15H19N2O5;NM+T-NH3-HPO3", + + "C:C5H9N;NM", + "C:C9H14N4O1;NM+C'", + "C:C9H12N4;NM+C'-H2O", + "C:C14H23N4O7P1;NM+C", + "C:C14H21N4O6P1;NM+C-H2O", + "C:C14H20N4O3;NM+C-H3PO4", + "C:C14H22N4O4;NM+C-HPO3", + + "G:C5H9N1;NM", + "G:C10H14N6O1;NM+G'", + "G:C10H12N6;NM+G'-H2O", + "G:C10H11N5O1;NM+G'-NH3", + "G:C15H23N6O7P1;NM+G", + "G:C15H21N6O6P1;NM+G-H2O", + "G:C15H22N6O4;NM+G-HPO3", + "G:C15H20N6O3;NM+G-H3PO4", + "G:C15H20N5O7P1;NM+G-NH3", + "G:C15H19N5O4;NM+G-NH3-HPO3", + + "A:C5H9N1;NM", + "A:C10H14N6;NM+A'", + "A:C10H11N5;NM+A'-NH3", + "A:C15H23N6O6P1;NM+A", + "A:C15H20N6O2;NM+A-H3PO4", + "A:C15H21N6O5P1;NM+A-H2O", + "A:C15H22N6O3;NM+A-HPO3", + "A:C15H20N5O6P1;NM+A-NH3", + "A:C15H19N5O3;NM+A-NH3-HPO3" + }; + + static constexpr std::array modifications_DNA_NM_PASE + {"T:+C5H9N1", + "T:+C5H9N1-H2O", "T:+C5H9N1-HPO3", "T:+C5H9N1-H3PO4", "T:+C5H9N1-H2O-H2O", "T:+C5H9N1-H3PO4-H2O", - "T:+C5H9N1-H2O", - "T:+C5H9N1-NH3-HPO3", + "G:+C5H9N1", + "G:+C5H9N1-H2O", "G:+C5H9N1-HPO3", "G:+C5H9N1-H3PO4", "G:+C5H9N1-H2O-H2O", "G:+C5H9N1-H3PO4-H2O", - "G:+C5H9N1-H2O", "G:+C5H9N1-NH3", "G:+C5H9N1-NH3-HPO3", + "C:+C5H9N1", "C:+C5H9N1-H2O", "C:+C5H9N1-HPO3", @@ -699,6 +1166,7 @@ class OpenNuXL : "C:+C5H9N1-H3PO4-H2O", "C:+C5H9N1-NH3", "C:+C5H9N1-NH3-HPO3", + "A:+C5H9N1", "A:+C5H9N1-H2O", "A:+C5H9N1-H3PO4-H2O", @@ -709,7 +1177,7 @@ class OpenNuXL : "A:+C5H9N1-NH3-HPO3" }; - static constexpr std::array fragments_DNA_NM + static constexpr std::array fragments_DNA_NM_PASE { "T:C5H9N1;NM", "T:C14H19N3O5;NM+T-H3PO4", "T:C10H15N3O2;NM+T'", @@ -720,6 +1188,7 @@ class OpenNuXL : "T:C10H12N2O2;NM+T'", "T:C15H20N2O8P1;NM+T-NH3", "T:C15H19N2O5;NM+T-NH3-HPO3", + "C:C5H9N;NM", "C:C9H14N4O1;NM+C'", "C:C9H12N4;NM+C'-H2O", @@ -727,6 +1196,7 @@ class OpenNuXL : "C:C14H21N4O6P1;NM+C-H2O", "C:C14H20N4O3;NM+C-H3PO4", "C:C14H22N4O4;NM+C-HPO3", + "G:C5H9N1;NM", "G:C10H14N6O1;NM+G'", "G:C10H12N6;NM+G'-H2O", @@ -737,6 +1207,7 @@ class OpenNuXL : "G:C15H20N6O3;NM+G-H3PO4", "G:C15H20N5O7P1;NM+G-NH3", "G:C15H19N5O4;NM+G-NH3-HPO3", + "A:C5H9N1;NM", "A:C10H14N6;NM+A'", "A:C10H11N5;NM+A'-NH3", @@ -745,7 +1216,8 @@ class OpenNuXL : "A:C15H21N6O5P1;NM+A-H2O", "A:C15H22N6O3;NM+A-HPO3", "A:C15H20N5O6P1;NM+A-NH3", - "A:C15H19N5O3;NM+A-NH3-HPO3"}; + "A:C15H19N5O3;NM+A-NH3-HPO3" + }; static constexpr std::array DNA_nucleotides {"A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P"}; // the mono-phosphates static constexpr std::array RNA_nucleotides {"A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"}; @@ -794,6 +1266,12 @@ class OpenNuXL : modifications = StringList(modifications_RNA_UV_4SU.begin(), modifications_RNA_UV_4SU.end()); can_cross_link = "S"; } + else if (p == "RNA-DEB (+Pase)") + { + modifications = StringList(modifications_RNA_DEB_PASE.begin(), modifications_RNA_DEB_PASE.end()); + fragment_adducts = StringList(fragments_RNA_DEB_PASE.begin(), fragments_RNA_DEB_PASE.end()); + can_cross_link = "UCGA"; + } else if (p == "RNA-DEB") { modifications = StringList(modifications_RNA_DEB.begin(), modifications_RNA_DEB.end()); @@ -806,12 +1284,30 @@ class OpenNuXL : fragment_adducts = StringList(fragments_DNA_DEB.begin(), fragments_DNA_DEB.end()); can_cross_link = "CTGA"; } + else if (p == "DNA-DEB (+Pase)") + { + modifications = StringList(modifications_DNA_DEB_PASE.begin(), modifications_DNA_DEB_PASE.end()); + fragment_adducts = StringList(fragments_DNA_DEB_PASE.begin(), fragments_DNA_DEB_PASE.end()); + can_cross_link = "CTGA"; + } + else if (p == "RNA-NM (+Pase)") + { + modifications = StringList(modifications_RNA_NM_PASE.begin(), modifications_RNA_NM_PASE.end()); + fragment_adducts = StringList(fragments_RNA_NM_PASE.begin(), fragments_RNA_NM_PASE.end()); + can_cross_link = "UCGA"; + } else if (p == "RNA-NM") { modifications = StringList(modifications_RNA_NM.begin(), modifications_RNA_NM.end()); fragment_adducts = StringList(fragments_RNA_NM.begin(), fragments_RNA_NM.end()); can_cross_link = "UCGA"; } + else if (p == "DNA-NM (+Pase)") + { + modifications = StringList(modifications_DNA_NM_PASE.begin(), modifications_DNA_NM_PASE.end()); + fragment_adducts = StringList(fragments_DNA_NM_PASE.begin(), fragments_DNA_NM_PASE.end()); + can_cross_link = "TCGA"; + } else if (p == "DNA-NM") { modifications = StringList(modifications_DNA_NM.begin(), modifications_DNA_NM.end()); @@ -1161,12 +1657,14 @@ class OpenNuXL : float& im_MIC, size_t& n_theoretical_peaks) { +#ifdef FRAGMENT_FREQ_SCALING static std::vector a_ = {0.6381814842871244,0.5757708524966219,0.3527782831613766,0.5540067995825595,0.5937077770271472,0.44059687579253287,0.5225166639570802,0.38841395620372815,0.3030517328354761,0.30979251695059956,0.30364346970241557,0.34222974087638314,0.21622567124817516,0.24461462554326147,0.25749353729143076,0.24628219274901375,0.13784446820799334,0.1495672137250644,0.2962157379587473,0.10986006002310685,0.1351953897278425,0.1278257687841041,0.30540105664584627,0.22667644652579907,0.18995271867612293,0.11525992655496903,0.22667644652579907,0.22667644652579907,0.3695782162734005,0.3695782162734005,0.5396963997850618,0.3695782162734005,0.38473739338620383,0.40192864687860225,0.41911990037100066,0.4387234158726692,0.4625932410429686,0.486463066213268,0.5103328913835674,0.5103328913835674,0.5103328913835674, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,}; static std::vector b_ = {0.36098796076403716,0.4347832206269399,0.5099710884346794,0.5179672293483799,0.5631123880294966,0.5533361427988034,0.5743842109687725,0.5423494643601069,0.5760269552782373,0.5036297443627675,0.4392665770184666,0.4555728357147309,0.44068578203629283,0.4818153581717703,0.36060791092937267,0.2209935596478243,0.20127921570150337,0.11845946442071022,0.07389126171037678,0.05773828326056386,0.05017396259908622,0.04637657640949555,0.16961055844449469,0.06798833158684754,0.3170397996809263,0.3380269790757273,0.40506200961781824,0.17955033881656035,0.4337336336589538,0.5052618285906718,0.6050407460304126,0.6050407460304126,0.33802697907572726,0.47153386255306995,0.6050407460304126,0.6050407460304126,0.6050407460304126,0.6050407460304126,0.6050407460304126,0.6050407460304126,0.6050407460304126, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,}; static std::vector y_ = {0.2565006415119941,0.45945372412717844,0.5115897779268463,0.5755301366035181,0.5848527137044559,0.5930609869981058,0.6076345273266521,0.6200719791091611,0.6136770720442932,0.6146578764556351,0.6279320448204195,0.6391734877807232,0.6108431180748586,0.5674428548097566,0.5129822532754515,0.6840850182019967,0.5483712842406266,0.24344021427549448,0.35994473654661996,0.4434850423849219,0.452735096428622,0.25291947015843297,0.3767693801420614,0.5301810038419658,0.21555832324685273,0.23211081378876122,0.2872560096622122,0.2872560096622122,0.3767693801420614,0.5473238809294039,0.47556492012642165,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614,0.3767693801420614, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,}; +#endif OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); @@ -1210,7 +1708,9 @@ static std::vector y_ = {0.2565006415119941,0.45945372412717844,0.511589 if (!peak_matched[index]) { double intensity = exp_spectrum[index].getIntensity(); +#ifdef FRAGMENT_FREQ_SCALING intensity *= b_[i]; ////////////////////////////////// fragment background freq scaling +#endif dot_product += intensity; b_mean_err += Math::getPPMAbs(exp_mz, theo_mz); b_ions[i] += intensity; @@ -1248,7 +1748,9 @@ static std::vector y_ = {0.2565006415119941,0.45945372412717844,0.511589 if (!peak_matched[index]) { double intensity = exp_spectrum[index].getIntensity(); +#ifdef FRAGMENT_FREQ_SCALING intensity *= a_[i]; ////////////////////////////////// fragment background freq scaling +#endif dot_product += intensity; a_ions[i] += intensity; ++matches; @@ -1281,8 +1783,9 @@ static std::vector y_ = {0.2565006415119941,0.45945372412717844,0.511589 if (!peak_matched[index]) { double intensity = exp_spectrum[index].getIntensity(); +#ifdef FRAGMENT_FREQ_SCALING intensity *= y_[i]; ////////////////////////////////// fragment background freq scaling - +#endif y_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; y_ions[N-1 - i] += intensity; @@ -1571,10 +2074,12 @@ static std::vector y_ = {0.2565006415119941,0.45945372412717844,0.511589 size_t& n_theoretical_peaks/*, bool is_decoy*/) { - +#ifdef FRAGMENT_FREQ_SCALING static std::vector xl_a_ = {0.3659528914710744,0.47861728235068857,0.42071800758257055,0.5033640127522735,0.5895282639501609,0.49264930296695003,0.5324411204304591,0.48417463865923027,0.5511271154003025,0.5286803949442149,0.7173140531939944,0.336435471054921,0.4859101632376203,0.5024262214061576,0.46840208095976715,0.40809322953700483,0.3167094903810921,0.18129098288335982,0.4189105949805667,0.3330045922905184,0.3126071182614005,0.0650657360415093,0.40059551576627994,0.24183385621259657,0.17535844006882048,0.28364985698456463,0.433598827728014,0.27286545915347155,0.17535844006882048,0.24183385621259657,0.16767660150073574,0.32361968601164226,0.656809394243162,0.5729006723867871,0.4889919505304121,0.656809394243162,0.7021597756570445,0.7475101570709268,0.7928605384848093,0.7928605384848093,0.7928605384848093}; static std::vector xl_b_ = {0.2491938528289777,0.3856151839213907,0.3647776031187359,0.5407667409164766,0.48483561551239046,0.545482943034812,0.44176624959405336,0.4892070682435069,0.5821888866263324,0.5283814756892558,0.5874975667022032,0.5254550930392076,0.6008338026815329,0.6255675366401964,0.5644205635354829,0.4547628038391301,0.3373921521612854,0.32736271323930605,0.29693905198602577,0.4331622745676728,0.2866614892568747,0.41334354567005543,0.26789101676894134,0.15648636150792897,0.03829355836488023,0.051609876958974295,0.06627620698070251,0.07546738423116832,0.11156988263191558,0.32875347958219475,0.14034341782502044,0.1891158141543777,0.28984234629777234,0.28984234629777234,0.28984234629777234,0.3524087974901858,0.3524087974901858,0.3524087974901858,0.3524087974901858,0.3524087974901858,0.3524087974901858}; static std::vector xl_y_ = {0.2222310518617074,0.22733216758392177,0.35054745332681947,0.37174426433751473,0.41759826478801526,0.4269329894992057,0.4705619772415399,0.552562608306239,0.6461531416854231,0.5530968264015448,0.6025099662697077,0.5478810430654834,0.5571688470181058,0.5504295835175378,0.5390253808536244,0.4847596410095063,0.5018553373891388,0.473181377276754,0.5860391279941947,0.5556416220543001,0.3859448483873362,0.651387747360435,0.516376393935597,0.4093617866644474,0.4469048380712779,0.2713822504471235,0.24260619760761046,0.2337540058421485,0.319634600171193,0.35700263742531846,0.4479621597068155,0.17596775433173067,0.34805080737787986,0.3052687956612212,0.26248678394456265,0.34805080737787986,0.34805080737787986,0.34805080737787986,0.34805080737787986,0.34805080737787986,0.34805080737787986}; +#endif + OPENMS_PRECONDITION(exp_spectrum.size() >= 1, "Experimental spectrum empty."); OPENMS_PRECONDITION(exp_charges.size() == exp_spectrum.size(), "Error: HyperScore: #charges != #peaks in experimental spectrum."); OPENMS_PRECONDITION(intensity_sum.size() == partial_loss_template_z1_b_ions.size(), "Sum array needs to be of same size as b-ion array"); @@ -1680,7 +2185,9 @@ static std::vector xl_y_ = {0.2222310518617074,0.22733216758392177,0.350 } #endif double intensity = exp_spectrum[index].getIntensity(); +#ifdef FRAGMENT_FREQ_SCALING intensity *= xl_b_[i]; ////////////////////////////////// fragment background freq scaling +#endif b_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; b_ions[i] += intensity; @@ -1740,7 +2247,9 @@ static std::vector xl_y_ = {0.2222310518617074,0.22733216758392177,0.350 } #endif double intensity = exp_spectrum[index].getIntensity(); +#ifdef FRAGMENT_FREQ_SCALING intensity *= xl_a_[i]; ////////////////////////////////// fragment background freq scaling +#endif dot_product += intensity; a_ions[i] += intensity; peak_matched[index] = true; @@ -1795,7 +2304,9 @@ static std::vector xl_y_ = {0.2222310518617074,0.22733216758392177,0.350 } #endif double intensity = exp_spectrum[index].getIntensity(); - intensity = intensity * xl_y_[i]; ////////////////////////////////// fragment background freq scaling +#ifdef FRAGMENT_FREQ_SCALING + intensity *= xl_y_[i]; ////////////////////////////////// fragment background freq scaling +#endif y_mean_err += Math::getPPMAbs(exp_mz, theo_mz); dot_product += intensity; y_ions[N-1 - i] += intensity; From 6ca7fef282159aa0a575db0c53358e28fc22c122 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 3 Nov 2021 12:48:54 +0100 Subject: [PATCH 192/471] update presets --- src/utils/OpenNuXL.cpp | 156 +++++++++++++++++++++++++++-------------- 1 file changed, 102 insertions(+), 54 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index b26fb3d9cdd..6f36c14d2bc 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -263,32 +263,38 @@ class OpenNuXL : static constexpr double MIN_TOTAL_LOSS_IONS = 1; // minimum number of matches to unshifted ions static constexpr double MIN_SHIFTED_IONS = 1; // minimum number of matches to shifted ions (applies to XLs only) - static constexpr std::array modifications_RNA_UV_PASE + static constexpr std::array modifications_RNA_UV_PASE {"U:", "U:-H2O", - "U:-H3PO4", "U:-HPO3", + "U:-H3PO4", "C:", "C:-NH3", "C:-H2O", - "C:-NH3-HPO3", "C:-H3PO4", "C:-HPO3", + "C:-NH3-HPO3", + "C:-NH3-H2O", + "C:-NH3-H3PO4", "G:", "G:-H2O", "G:-NH3", "G:-H3PO4", - "G:-NH3-HPO3", "G:-HPO3", + "G:-NH3-HPO3", + "G:-NH3-H2O", + "G:-NH3-H3PO4", "A:", "A:-H2O", "A:-HPO3" "A:-H3PO4", "A:-NH3", - "A:-NH3-HPO3" + "A:-NH3-H2O", + "A:-NH3-HPO3", + "A:-NH3-H3PO4" }; static constexpr std::array fragments_RNA_UV_PASE @@ -329,21 +335,24 @@ class OpenNuXL : "A:C5H5N5;A'", "A:C5H2N4;A'-NH3" }; - static constexpr std::array modifications_RNA_UV + static constexpr std::array modifications_RNA_UV {"U:", "U:-H2O", "C:", "C:-NH3", "C:-H2O", + "C:-NH3-H2O", "G:", "G:-H2O", "G:-NH3", + "G:-NH3-H2O", "A:", "A:-H2O", - "A:-NH3" + "A:-NH3", + "A:-NH3-H2O" }; static constexpr std::array fragments_RNA_UV @@ -386,12 +395,11 @@ class OpenNuXL : }; - static constexpr std::array modifications_RNA_UV_4SU_PASE + static constexpr std::array modifications_RNA_UV_4SU_PASE { "S:", "S:-H2O", "S:-H2O-HPO3", "S:-HPO3", - "S:-H2S+HPO3", "S:-H2S" }; @@ -414,12 +422,12 @@ class OpenNuXL : "C:C4H5N3O;C'", "C:C4H3N3;C'-H2O", "C:C4H2N2O;C'-NH3", + "C:C9H10N2O5;C-NH3-HPO3", "G:C10H14N5O8P;G", "G:C10H12N5O7P;G-H2O", "G:C10H11N4O8P;G-NH3", "G:C10H13N5O5;G-HPO3", - "C:C9H10N2O5;C-NH3-HPO3", "G:C10H10N4O5;G-NH3-HPO3", "G:C10H11N5O4;G-H3PO4", "G:C5H5N5O;G'", @@ -436,10 +444,9 @@ class OpenNuXL : "A:C5H2N4;A'-NH3" }; - static constexpr std::array modifications_RNA_UV_4SU + static constexpr std::array modifications_RNA_UV_4SU { "S:", "S:-H2O", - "S:-H2S+HPO3", "S:-H2S" }; @@ -485,29 +492,30 @@ class OpenNuXL : }; - static constexpr std::array modifications_DNA_UV + static constexpr std::array modifications_DNA_UV {"T:", "T:-H2O", - "T:+C5H7O5P", // + dribose-H2O - "T:-C5H6N2O2", "G:", "G:-H2O", "G:-NH3", - "G:+C5H7O5P", - "G:-C5H5N5O", + "G:-NH3-H2O", - "A:-NH3", - "A:+C5H7O5P", "A:", + "A:-NH3", "A:-H2O", - "A:-C5H5N5", + "A:-NH3-H2O", "C:", "C:-H2O", "C:-NH3", - "C:+C5H7O5P", - "C:-C4H5N3O" // loss of base -> only dribose remains + "C:-NH3-H2O", + + // loss of base -> only dribose remains + "T:-C5H6N2O2", + "G:-C5H5N5O", + "A:-C5H5N5", + "C:-C4H5N3O" }; static constexpr std::array fragments_DNA_UV @@ -561,38 +569,41 @@ class OpenNuXL : "T:C5H8O3;C5H9O6P-HPO3" }; - static constexpr std::array modifications_DNA_UV_PASE + static constexpr std::array modifications_DNA_UV_PASE {"T:", "T:-H2O", - "T:-H2O-HPO3", + "T:-H3PO4", "T:-HPO3", "A:", "A:-H2O", - "A:-H2O-HPO3", + "A:-H3PO4", "A:-HPO3", "A:-NH3", + "A:-NH3-H2O", + "A:-NH3-HPO3", + "A:-NH3-H3PO4", "G:", "G:-H2O", - "G:-NH3", + "G:-H3PO4", "G:-HPO3", - "G:-H2O-HPO3", + "G:-NH3", + "G:-NH3-H2O", "G:-NH3-HPO3", + "G:-NH3-H3PO4", "C:", "C:-H2O", + "C:-H3PO4", + "C:-HPO3", "C:-NH3", - "C:-H2O-HPO3", - "C:-NH3", + "C:-NH3-H2O", "C:-NH3-HPO3", + "C:-NH3-H3PO4", - "T:+C5H7O5P", // + dribose-H2O - "A:+C5H7O5P", - "G:+C5H7O5P", - "C:+C5H7O5P", - - "C:-C4H5N3O", // loss of base -> only dribose remains + // loss of base -> only dribose remains + "C:-C4H5N3O", "T:-C5H6N2O2", "G:-C5H5N5O", "A:-C5H5N5" @@ -649,7 +660,7 @@ class OpenNuXL : "T:C5H8O3;C5H9O6P-HPO3" }; - static constexpr std::array modifications_RNA_DEB_PASE + static constexpr std::array modifications_RNA_DEB_PASE { "U:+C4H6O2", "U:+C4H6O2-H2O", "U:+C4H6O2-HPO3", @@ -664,7 +675,9 @@ class OpenNuXL : "G:+C4H6O2-H2O-H2O", "G:+C4H6O2-H3PO4-H2O", "G:+C4H6O2-NH3", + "G:+C4H6O2-NH3-H2O", "G:+C4H602-NH3-HPO3", + "G:+C4H6O2-NH3-H3PO4", "C:+C4H6O2", "C:+C4H6O2-H2O", @@ -673,16 +686,20 @@ class OpenNuXL : "C:+C4H6O2-H2O-H2O", "C:+C4H6O2-H3PO4-H2O", "C:+C4H6O2-NH3", + "C:+C4H6O2-NH3-H2O", "C:+C4H602-NH3-HPO3", + "C:+C4H6O2-NH3-H3PO4", "A:+C4H6O2", "A:+C4H6O2-H2O", + "A:+C4H6O2-H2O-H2O", "A:+C4H6O2-HPO3", "A:+C4H6O2-H3PO4", - "A:+C4H6O2-H2O-H2O", "A:+C4H6O2-H3PO4-H2O", "A:+C4H6O2-NH3", - "A:+C4H602-NH3-HPO3" + "A:+C4H6O2-NH3-H2O", + "A:+C4H602-NH3-HPO3", + "A:+C4H6O2-NH3-H3PO4" }; static constexpr std::array fragments_RNA_DEB_PASE @@ -728,7 +745,7 @@ class OpenNuXL : "A:C14H17N4O9;DEB+A-NH3" }; - static constexpr std::array modifications_RNA_DEB + static constexpr std::array modifications_RNA_DEB { "U:+C4H6O2", "U:+C4H6O2-H2O", "U:+C4H6O2-H2O-H2O", @@ -737,18 +754,19 @@ class OpenNuXL : "G:+C4H6O2-H2O", "G:+C4H6O2-H2O-H2O", "G:+C4H6O2-NH3", + "G:+C4H6O2-NH3-H2O", "C:+C4H6O2", "C:+C4H6O2-H2O", "C:+C4H6O2-H2O-H2O", - "C:+C4H6O2-H2O", "C:+C4H6O2-NH3", + "C:+C4H6O2-NH3-H2O", "A:+C4H6O2", "A:+C4H6O2-H2O", "A:+C4H6O2-H2O-H2O", - "A:+C4H6O2-H2O", - "A:+C4H6O2-NH3" + "A:+C4H6O2-NH3", + "A:+C4H6O2-NH3-H2O" }; static constexpr std::array fragments_RNA_DEB @@ -794,8 +812,8 @@ class OpenNuXL : "A:C14H17N4O9;DEB+A-NH3" }; - static constexpr std::array modifications_DNA_DEB - { // adapted from Fanni + water losses + static constexpr std::array modifications_DNA_DEB + { "T:+C4H6O2", "T:+C4H6O2-H2O", "T:+C4H6O2-H2O-H2O", @@ -804,16 +822,19 @@ class OpenNuXL : "G:+C4H6O2-H2O", "G:+C4H6O2-H2O-H2O", "G:+C4H6O2-NH3", + "G:+C4H6O2-NH3-H2O", "C:+C4H6O2", "C:+C4H6O2-H2O", "C:+C4H6O2-H2O-H2O", "C:+C4H6O2-NH3", + "C:+C4H6O2-NH3-H2O", "A:+C4H6O2", - "A:+C4H6O2-H2O" + "A:+C4H6O2-H2O", "A:+C4H6O2-H2O-H2O", - "A:+C4H6O2-NH3" + "A:+C4H6O2-NH3", + "A:+C4H6O2-NH3-H2O" }; static constexpr std::array fragments_DNA_DEB @@ -864,7 +885,7 @@ class OpenNuXL : // "A:C14H17N5O4;DEB+A-H3PO4" // C4H6O2 + C10H14N5O6P - H3PO4 }; - static constexpr std::array modifications_DNA_DEB_PASE + static constexpr std::array modifications_DNA_DEB_PASE // adapted from Fanni + water losses {"T:+C4H6O2", "T:+C4H6O2-HPO3", @@ -880,7 +901,9 @@ class OpenNuXL : "G:+C4H6O2-H3PO4-H2O", "G:+C4H6O2-H2O", "G:+C4H6O2-NH3", + "G:+C4H6O2-NH3-H2O", "G:+C4H6O2-NH3-HPO3", + "G:+C4H6O2-NH3-H3PO4", "C:+C4H6O2", "C:+C4H6O2-H2O", @@ -888,8 +911,10 @@ class OpenNuXL : "C:+C4H6O2-H3PO4", "C:+C4H6O2-H2O-H2O", "C:+C4H6O2-H3PO4-H2O", + "C:+C4H6O2-NH3-H2O", "C:+C4H6O2-NH3", "C:+C4H6O2-NH3-HPO3", + "C:+C4H6O2-NH3-H3PO4", "A:+C4H6O2", "A:+C4H6O2-H2O", @@ -898,7 +923,9 @@ class OpenNuXL : "A:+C4H6O2-H3PO4", "A:+C4H6O2-HPO3", "A:+C4H6O2-NH3", - "A:+C4H6O2-NH3-HPO3" + "A:+C4H6O2-NH3-H2O", + "A:+C4H6O2-NH3-HPO3", + "A:+C4H6O2-NH3-H3PO4" }; static constexpr std::array fragments_DNA_DEB_PASE @@ -947,7 +974,7 @@ class OpenNuXL : }; - static constexpr std::array modifications_RNA_NM_PASE + static constexpr std::array modifications_RNA_NM_PASE {"U:+C5H9N1", "U:+C5H9N1-HPO3", "U:+C5H9N1-H2O", @@ -962,6 +989,9 @@ class OpenNuXL : "G:+C5H9N1-H2O-H2O", "G:+C5H9N1-H3PO4-H2O", "G:+C5H9N1-NH3", + "G:+C5H9N1-NH3-H2O", + "G:+C5H9N1-NH3-HPO3" + "G:+C5H9N1-NH3-H3PO4", "C:+C5H9N1", "C:+C5H9N1-HPO3", @@ -970,6 +1000,9 @@ class OpenNuXL : "C:+C5H9N1-H2O-H2O", "C:+C5H9N1-H3PO4-H2O", "C:+C5H9N1-NH3", + "C:+C5H9N1-NH3-H2O", + "C:+C5H9N1-NH3-HPO3" + "C:+C5H9N1-NH3-H3PO4", "A:+C5H9N1", "A:+C5H9N1-HPO3", @@ -977,7 +1010,10 @@ class OpenNuXL : "A:+C5H9N1-H3PO4", "A:+C5H9N1-H2O-H2O", "A:+C5H9N1-H3PO4-H2O", - "A:+C5H9N1-NH3" + "A:+C5H9N1-NH3", + "A:+C5H9N1-NH3-H2O", + "A:+C5H9N1-NH3-HPO3" + "A:+C5H9N1-NH3-H3PO4" }; static constexpr std::array fragments_RNA_NM_PASE @@ -1018,7 +1054,7 @@ class OpenNuXL : "A:C15H22N6O4;NM+A-HPO3" }; - static constexpr std::array modifications_RNA_NM + static constexpr std::array modifications_RNA_NM {"U:+C5H9N1", "U:+C5H9N1-H2O-H2O", "U:+C5H9N1-H2O", @@ -1027,16 +1063,19 @@ class OpenNuXL : "G:+C5H9N1-H2O-H2O", "G:+C5H9N1-H2O", "G:+C5H9N1-NH3", + "G:+C5H9N1-NH3-H2O", "C:+C5H9N1", "C:+C5H9N1-H2O", "C:+C5H9N1-H2O-H2O", "C:+C5H9N1-NH3", + "C:+C5H9N1-NH3-H2O", "A:+C5H9N1", "A:+C5H9N1-H2O", "A:+C5H9N1-H2O-H2O", - "A:+C5H9N1-NH3" + "A:+C5H9N1-NH3", + "A:+C5H9N1-NH3-H2O" }; static constexpr std::array fragments_RNA_NM @@ -1078,7 +1117,7 @@ class OpenNuXL : }; - static constexpr std::array modifications_DNA_NM + static constexpr std::array modifications_DNA_NM {"T:+C5H9N1", "T:+C5H9N1-H2O-H2O", "T:+C5H9N1-H2O", @@ -1087,16 +1126,19 @@ class OpenNuXL : "G:+C5H9N1-H2O-H2O", "G:+C5H9N1-H2O", "G:+C5H9N1-NH3", + "G:+C5H9N1-NH3-H2O", "C:+C5H9N1", "C:+C5H9N1-H2O", "C:+C5H9N1-H2O-H2O", "C:+C5H9N1-NH3", + "C:+C5H9N1-NH3-H2O", "A:+C5H9N1", "A:+C5H9N1-H2O", "A:+C5H9N1-H2O-H2O", "A:+C5H9N1-NH3", + "A:+C5H9N1-NH3-H2O", }; static constexpr std::array fragments_DNA_NM @@ -1141,7 +1183,7 @@ class OpenNuXL : "A:C15H19N5O3;NM+A-NH3-HPO3" }; - static constexpr std::array modifications_DNA_NM_PASE + static constexpr std::array modifications_DNA_NM_PASE {"T:+C5H9N1", "T:+C5H9N1-H2O", "T:+C5H9N1-HPO3", @@ -1156,7 +1198,9 @@ class OpenNuXL : "G:+C5H9N1-H2O-H2O", "G:+C5H9N1-H3PO4-H2O", "G:+C5H9N1-NH3", + "G:+C5H9N1-NH3-H2O", "G:+C5H9N1-NH3-HPO3", + "G:+C5H9N1-NH3-H3PO4", "C:+C5H9N1", "C:+C5H9N1-H2O", @@ -1166,6 +1210,8 @@ class OpenNuXL : "C:+C5H9N1-H3PO4-H2O", "C:+C5H9N1-NH3", "C:+C5H9N1-NH3-HPO3", + "C:+C5H9N1-NH3-H2O", + "C:+C5H9N1-NH3-H3PO4", "A:+C5H9N1", "A:+C5H9N1-H2O", @@ -1175,6 +1221,8 @@ class OpenNuXL : "A:+C5H9N1-HPO3", "A:+C5H9N1-NH3", "A:+C5H9N1-NH3-HPO3" + "A:+C5H9N1-NH3-H2O", + "A:+C5H9N1-NH3-H3PO4", }; static constexpr std::array fragments_DNA_NM_PASE From ad649a74b724788367dd4a35db1dce070a49a288 Mon Sep 17 00:00:00 2001 From: timosachsenberg Date: Wed, 3 Nov 2021 14:26:38 +0100 Subject: [PATCH 193/471] fixed presets --- src/utils/OpenNuXL.cpp | 149 +++++++++++++++++++++++++++++++---------- 1 file changed, 112 insertions(+), 37 deletions(-) diff --git a/src/utils/OpenNuXL.cpp b/src/utils/OpenNuXL.cpp index 6f36c14d2bc..9ddaaa4e89b 100644 --- a/src/utils/OpenNuXL.cpp +++ b/src/utils/OpenNuXL.cpp @@ -289,7 +289,7 @@ class OpenNuXL : "A:", "A:-H2O", - "A:-HPO3" + "A:-HPO3", "A:-H3PO4", "A:-NH3", "A:-NH3-H2O", @@ -990,7 +990,7 @@ class OpenNuXL : "G:+C5H9N1-H3PO4-H2O", "G:+C5H9N1-NH3", "G:+C5H9N1-NH3-H2O", - "G:+C5H9N1-NH3-HPO3" + "G:+C5H9N1-NH3-HPO3", "G:+C5H9N1-NH3-H3PO4", "C:+C5H9N1", @@ -1001,7 +1001,7 @@ class OpenNuXL : "C:+C5H9N1-H3PO4-H2O", "C:+C5H9N1-NH3", "C:+C5H9N1-NH3-H2O", - "C:+C5H9N1-NH3-HPO3" + "C:+C5H9N1-NH3-HPO3", "C:+C5H9N1-NH3-H3PO4", "A:+C5H9N1", @@ -1012,7 +1012,7 @@ class OpenNuXL : "A:+C5H9N1-H3PO4-H2O", "A:+C5H9N1-NH3", "A:+C5H9N1-NH3-H2O", - "A:+C5H9N1-NH3-HPO3" + "A:+C5H9N1-NH3-HPO3", "A:+C5H9N1-NH3-H3PO4" }; @@ -1220,7 +1220,7 @@ class OpenNuXL : "A:+C5H9N1-H3PO4", "A:+C5H9N1-HPO3", "A:+C5H9N1-NH3", - "A:+C5H9N1-NH3-HPO3" + "A:+C5H9N1-NH3-HPO3", "A:+C5H9N1-NH3-H2O", "A:+C5H9N1-NH3-H3PO4", }; @@ -1272,16 +1272,27 @@ class OpenNuXL : static constexpr std::array DNA_mapping {"A->A", "C->C", "G->G", "T->T"}; static constexpr std::array RNA_mapping {"A->A", "C->C", "G->G", "U->U"}; + static constexpr std::array presets_names {"none", "RNA-UV (U)", "RNA-UV (UCGA)", "RNA-UV Pase (U)", "RNA-UV Pase (UCGA)", "RNA-UV (4SU)", "RNA-UV Pase (4SU)", "DNA-UV", "DNA-UV Pase", "RNA-DEB", "RNA-DEB Pase", "DNA-DEB", "DNA-DEB Pase", "RNA-NM", "RNA-NM Pase", "DNA-NM", "DNA-NM Pase"}; + protected: /// percolator feature set StringList feature_set_; - void getPresets_(const String& p, StringList& nucleotides, + void getPresets_(const String& p, + StringList& nucleotides, StringList& mapping, StringList& modifications, StringList& fragment_adducts, String& can_cross_link) { + const StringList names(presets_names.begin(), presets_names.end()); + + // sanity check: preset name needs to be in the list of supported presets + if (auto it = find(names.begin(), names.end(), p); it == names.end()) + { + throw std::runtime_error("Error: unknown preset."); + } + // set NTs for RNA / DNA if (p.hasPrefix("RNA")) { @@ -1293,73 +1304,137 @@ class OpenNuXL : nucleotides = StringList(DNA_nucleotides.begin(), DNA_nucleotides.end()); mapping = StringList(DNA_mapping.begin(), DNA_mapping.end()); } - + + // initialize StringLists from constexpr arrays + StringList RNA_UV_modifications(std::begin(modifications_RNA_UV), std::end(modifications_RNA_UV)); + StringList RNA_UV_fragments(fragments_RNA_UV.begin(), fragments_RNA_UV.end()); + + StringList RNA_UV_PASE_modifications(modifications_RNA_UV_PASE.begin(), modifications_RNA_UV_PASE.end()); + StringList RNA_UV_PASE_fragments(fragments_RNA_UV_PASE.begin(), fragments_RNA_UV_PASE.end()); + + StringList DNA_UV_modifications(modifications_DNA_UV.begin(), modifications_DNA_UV.end()); + StringList DNA_UV_fragments(fragments_DNA_UV.begin(), fragments_DNA_UV.end()); + + StringList DNA_UV_PASE_modifications(modifications_DNA_UV_PASE.begin(), modifications_DNA_UV_PASE.end()); + StringList DNA_UV_PASE_fragments(fragments_DNA_UV_PASE.begin(), fragments_DNA_UV_PASE.end()); + + StringList RNA_UV_4SU_modifications(modifications_RNA_UV_4SU.begin(), modifications_RNA_UV_4SU.end()); + StringList RNA_UV_4SU_fragments(fragments_RNA_UV_4SU.begin(), fragments_RNA_UV_4SU.end()); + + StringList RNA_UV_4SU_PASE_modifications(modifications_RNA_UV_4SU_PASE.begin(), modifications_RNA_UV_4SU_PASE.end()); + StringList RNA_UV_4SU_PASE_fragments(fragments_RNA_UV_4SU_PASE.begin(), fragments_RNA_UV_4SU_PASE.end()); + + StringList RNA_DEB_modifications(modifications_RNA_DEB.begin(), modifications_RNA_DEB.end()); + StringList RNA_DEB_fragments(fragments_RNA_DEB.begin(), fragments_RNA_DEB.end()); + + StringList RNA_DEB_PASE_modifications(modifications_RNA_DEB_PASE.begin(), modifications_RNA_DEB_PASE.end()); + StringList RNA_DEB_PASE_fragments(fragments_RNA_DEB_PASE.begin(), fragments_RNA_DEB_PASE.end()); + + StringList DNA_DEB_modifications(modifications_DNA_DEB.begin(), modifications_DNA_DEB.end()); + StringList DNA_DEB_fragments(fragments_DNA_DEB.begin(), fragments_DNA_DEB.end()); + + StringList DNA_DEB_PASE_modifications(modifications_DNA_DEB_PASE.begin(), modifications_DNA_DEB_PASE.end()); + StringList DNA_DEB_PASE_fragments(fragments_DNA_DEB_PASE.begin(), fragments_DNA_DEB_PASE.end()); + + StringList RNA_NM_modifications(modifications_RNA_NM.begin(), modifications_RNA_NM.end()); + StringList RNA_NM_fragments(fragments_RNA_NM.begin(), fragments_RNA_NM.end()); + + StringList RNA_NM_PASE_modifications(modifications_RNA_NM_PASE.begin(), modifications_RNA_NM_PASE.end()); + StringList RNA_NM_PASE_fragments(fragments_RNA_NM_PASE.begin(), fragments_RNA_NM_PASE.end()); + + StringList DNA_NM_modifications(modifications_DNA_NM.begin(), modifications_DNA_NM.end()); + StringList DNA_NM_fragments(fragments_DNA_NM.begin(), fragments_DNA_NM.end()); + + StringList DNA_NM_PASE_modifications(modifications_DNA_NM_PASE.begin(), modifications_DNA_NM_PASE.end()); + StringList DNA_NM_PASE_fragments(fragments_DNA_NM_PASE.begin(), fragments_DNA_NM_PASE.end()); + + // set precursor + fragment adducts and cross-linked nucleotide if (p == "RNA-UV (U)" || p == "RNA-UV (UCGA)") { - modifications = StringList(modifications_RNA_UV.begin(), modifications_RNA_UV.end()); - fragment_adducts = StringList(fragments_RNA_UV.begin(), fragments_RNA_UV.end()); + modifications = RNA_UV_modifications; + fragment_adducts = RNA_UV_fragments; + can_cross_link = (p == "RNA-UV (U)") ? "U" : "UCGA" ; + } + else if (p == "RNA-UV Pase (U)" || p == "RNA-UV Pase (UCGA)") + { + modifications = RNA_UV_PASE_modifications; + fragment_adducts = RNA_UV_PASE_fragments; can_cross_link = (p == "RNA-UV (U)") ? "U" : "UCGA" ; } else if (p == "DNA-UV") { - modifications = StringList(modifications_DNA_UV.begin(), modifications_DNA_UV.end()); - fragment_adducts = StringList(fragments_DNA_UV.begin(), fragments_DNA_UV.end()); + modifications = DNA_UV_modifications; + fragment_adducts = DNA_UV_fragments; + can_cross_link = "CTGA"; + } + else if (p == "DNA-UV Pase") + { + modifications = DNA_UV_PASE_modifications; + fragment_adducts = DNA_UV_PASE_fragments; can_cross_link = "CTGA"; } else if (p == "RNA-UV (4SU)") { nucleotides.push_back("S=C9H13N2O8PS"); // include thio-U mapping.push_back("S->S"); - fragment_adducts = StringList(fragments_RNA_UV_4SU.begin(), fragments_RNA_UV_4SU.end()); - modifications = StringList(modifications_RNA_UV_4SU.begin(), modifications_RNA_UV_4SU.end()); + modifications = RNA_UV_4SU_modifications; + fragment_adducts = RNA_UV_4SU_fragments; can_cross_link = "S"; } - else if (p == "RNA-DEB (+Pase)") + else if (p == "RNA-UV Pase (4SU)") { - modifications = StringList(modifications_RNA_DEB_PASE.begin(), modifications_RNA_DEB_PASE.end()); - fragment_adducts = StringList(fragments_RNA_DEB_PASE.begin(), fragments_RNA_DEB_PASE.end()); - can_cross_link = "UCGA"; + nucleotides.push_back("S=C9H13N2O8PS"); // include thio-U + mapping.push_back("S->S"); + modifications = RNA_UV_4SU_PASE_modifications; + fragment_adducts = RNA_UV_4SU_PASE_fragments; + can_cross_link = "S"; } else if (p == "RNA-DEB") { - modifications = StringList(modifications_RNA_DEB.begin(), modifications_RNA_DEB.end()); - fragment_adducts = StringList(fragments_RNA_DEB.begin(), fragments_RNA_DEB.end()); + modifications = RNA_DEB_modifications; + fragment_adducts = RNA_DEB_fragments; + can_cross_link = "UCGA"; + } + else if (p == "RNA-DEB Pase") + { + modifications = RNA_DEB_PASE_modifications; + fragment_adducts = RNA_DEB_PASE_fragments; can_cross_link = "UCGA"; } else if (p == "DNA-DEB") { - modifications = StringList(modifications_DNA_DEB.begin(), modifications_DNA_DEB.end()); - fragment_adducts = StringList(fragments_DNA_DEB.begin(), fragments_DNA_DEB.end()); + modifications = DNA_DEB_modifications; + fragment_adducts = DNA_DEB_fragments; can_cross_link = "CTGA"; } - else if (p == "DNA-DEB (+Pase)") + else if (p == "DNA-DEB Pase") { - modifications = StringList(modifications_DNA_DEB_PASE.begin(), modifications_DNA_DEB_PASE.end()); - fragment_adducts = StringList(fragments_DNA_DEB_PASE.begin(), fragments_DNA_DEB_PASE.end()); + modifications = DNA_DEB_PASE_modifications; + fragment_adducts = DNA_DEB_PASE_fragments; can_cross_link = "CTGA"; } - else if (p == "RNA-NM (+Pase)") + else if (p == "RNA-NM") { - modifications = StringList(modifications_RNA_NM_PASE.begin(), modifications_RNA_NM_PASE.end()); - fragment_adducts = StringList(fragments_RNA_NM_PASE.begin(), fragments_RNA_NM_PASE.end()); + modifications = RNA_NM_modifications; + fragment_adducts = RNA_NM_fragments; can_cross_link = "UCGA"; } - else if (p == "RNA-NM") + else if (p == "RNA-NM Pase") { - modifications = StringList(modifications_RNA_NM.begin(), modifications_RNA_NM.end()); - fragment_adducts = StringList(fragments_RNA_NM.begin(), fragments_RNA_NM.end()); + modifications = RNA_NM_PASE_modifications; + fragment_adducts = RNA_NM_PASE_fragments; can_cross_link = "UCGA"; } - else if (p == "DNA-NM (+Pase)") + else if (p == "DNA-NM") { - modifications = StringList(modifications_DNA_NM_PASE.begin(), modifications_DNA_NM_PASE.end()); - fragment_adducts = StringList(fragments_DNA_NM_PASE.begin(), fragments_DNA_NM_PASE.end()); + modifications = DNA_NM_modifications; + fragment_adducts = DNA_NM_fragments; can_cross_link = "TCGA"; } - else if (p == "DNA-NM") + else if (p == "DNA-NM Pase") { - modifications = StringList(modifications_DNA_NM.begin(), modifications_DNA_NM.end()); - fragment_adducts = StringList(fragments_DNA_NM.begin(), fragments_DNA_NM.end()); + modifications = DNA_NM_PASE_modifications; + fragment_adducts = DNA_NM_PASE_fragments; can_cross_link = "TCGA"; } } @@ -1446,7 +1521,7 @@ class OpenNuXL : registerStringOption_("RNPxl:presets", " - + @@ -21,24 +21,24 @@ - + - + - + - + - + - - + + From 9782985ea6b38f2104227b465292552446e258c5 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 22 Jan 2025 10:39:35 +0100 Subject: [PATCH 317/471] remove feature augmentation --- .../ANALYSIS/NUXL/NuXLFeatureAugmentation.h | 129 ------------------ .../OpenMS/ANALYSIS/NUXL/sources.cmake | 1 - .../ANALYSIS/NUXL/NuXLFeatureAugmentation.cpp | 9 -- src/openms/source/ANALYSIS/NUXL/sources.cmake | 1 - src/topp/OpenNuXL.cpp | 7 - 5 files changed, 147 deletions(-) delete mode 100644 src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLFeatureAugmentation.h delete mode 100644 src/openms/source/ANALYSIS/NUXL/NuXLFeatureAugmentation.cpp diff --git a/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLFeatureAugmentation.h b/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLFeatureAugmentation.h deleted file mode 100644 index 4dda5878124..00000000000 --- a/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLFeatureAugmentation.h +++ /dev/null @@ -1,129 +0,0 @@ -// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin -// SPDX-License-Identifier: BSD-3-Clause -// -// -------------------------------------------------------------------------- -// $Maintainer: Timo Sachsenberg $ -// $Authors: Timo Sachsenberg $ -// -------------------------------------------------------------------------- - -#pragma once - -#include -#include -#include - -#include -#include - -namespace OpenMS -{ - class OPENMS_DLLAPI NuXLFeatureAugmentation - { - public: - static void augment(std::vector& pep_ids, - std::vector positive_weights, - std::vector negative_weights) - { - // only for XLs? because they are fewer? - if (pep_ids.empty()) return; - - if (pep_ids[0].getHits().empty()) return; - - // feature names may not intersect between postive/negative constrained - std::sort(positive_weights.begin(), positive_weights.end()); - std::sort(negative_weights.begin(), negative_weights.end()); - std::vector v_intersection; - - std::set_intersection(positive_weights.begin(), positive_weights.end(), - negative_weights.begin(), negative_weights.end(), - std::back_inserter(v_intersection)); - - if (!v_intersection.empty()) throw std::runtime_error("Positive and negative weights may not overlap."); - - // use first PSM as template - auto p_template = pep_ids[0].getHits()[0]; - p_template.setScore(0); - std::vector keys; - p_template.getKeys(keys); - p_template.setMetaValue("NuXL:augmented", "true"); - - // clear scores of template - for (const auto& k : keys) - { - if (p_template.getMetaValue(k).valueType() == DataValue::INT_VALUE) p_template.setMetaValue(k, 0); - if (p_template.getMetaValue(k).valueType() == DataValue::DOUBLE_VALUE) p_template.setMetaValue(k, 0.0); - } - - // determine minium and maximum for each of the positive constrained features - std::map minima; - std::map maxima; - - for (const auto& k : positive_weights) - { - minima[k] = 1e32; - maxima[k] = -1e32; - } - - for (const auto& pid : pep_ids) - { - for (const auto& ph : pid.getHits()) - { - for (const auto& k : positive_weights) - { - auto dv = ph.getMetaValue(k); - if (dv.valueType() == DataValue::INT_VALUE) - { - if (minima[k] > (int)dv) minima[k] = (int)dv; - if (maxima[k] < (int)dv) maxima[k] = (int)dv; - }; - if (dv.valueType() == DataValue::DOUBLE_VALUE) - { - if (minima[k] > (double)dv) minima[k] = (double)dv; - if (maxima[k] < (double)dv) maxima[k] = (double)dv; - }; - } - } - } - - size_t c = 0; - // for each positive_weight feature, create one example with that feature set to max value - for (const auto& s : positive_weights) - { - auto p = p_template; - p.setMetaValue(s, maxima[s] + 1000.0 * (maxima[s] - minima[s])); // set feature value to >> maximum of observed ones - std::vector phs; - phs.push_back(p); - PeptideIdentification pid = pep_ids[0]; - pid.setRT(1e6 + c); // RT of augmented example - pid.setHits(phs); - pep_ids.push_back(pid); - ++c; - } - - // for each negative_weight feature, create one example with that feature set to min value - for (const auto& s : negative_weights) - { - auto p = p_template; - p.setMetaValue(s, minima[s] - 1000.0 * (maxima[s] - minima[s])); // set feature value to << min of observed ones - std::vector phs; - phs.push_back(p); - PeptideIdentification pid = pep_ids[0]; - pid.setRT(1e6 + c); // RT of augmented example - pid.setHits(phs); - pep_ids.push_back(pid); - ++c; - } - } - - static void removeAugmented(std::vector& pep_ids) - { - // remove augmented features again - for (auto& pid : pep_ids) - { - auto& phs = pid.getHits(); - phs.erase(remove_if(phs.begin(), phs.end(), [](const PeptideHit& ph){ return ph.metaValueExists("NuXL:augmented"); }), phs.end()); - } - } - }; -} - diff --git a/src/openms/include/OpenMS/ANALYSIS/NUXL/sources.cmake b/src/openms/include/OpenMS/ANALYSIS/NUXL/sources.cmake index 764d4642d93..fa7fccb1098 100644 --- a/src/openms/include/OpenMS/ANALYSIS/NUXL/sources.cmake +++ b/src/openms/include/OpenMS/ANALYSIS/NUXL/sources.cmake @@ -8,7 +8,6 @@ NuXLAnnotatedHit.h NuXLConstants.h NuXLDeisotoper.h NuXLFDR.h -NuXLFeatureAugmentation.h NuXLFragmentAdductDefinition.h NuXLFragmentAnnotationHelper.h NuXLFragmentIonGenerator.h diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLFeatureAugmentation.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLFeatureAugmentation.cpp deleted file mode 100644 index a5c83175676..00000000000 --- a/src/openms/source/ANALYSIS/NUXL/NuXLFeatureAugmentation.cpp +++ /dev/null @@ -1,9 +0,0 @@ -// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin -// SPDX-License-Identifier: BSD-3-Clause -// -// -------------------------------------------------------------------------- -// $Maintainer: Timo Sachsenberg $ -// $Authors: Timo Sachsenberg $ -// -------------------------------------------------------------------------- - -#include diff --git a/src/openms/source/ANALYSIS/NUXL/sources.cmake b/src/openms/source/ANALYSIS/NUXL/sources.cmake index 36d9243eaa4..460ac2a2607 100644 --- a/src/openms/source/ANALYSIS/NUXL/sources.cmake +++ b/src/openms/source/ANALYSIS/NUXL/sources.cmake @@ -6,7 +6,6 @@ set(sources_list NuXLAnnotateAndLocate.cpp NuXLDeisotoper.cpp NuXLFDR.cpp -NuXLFeatureAugmentation.cpp NuXLFragmentAdductDefinition.cpp NuXLFragmentAnnotationHelper.cpp NuXLFragmentIonGenerator.cpp diff --git a/src/topp/OpenNuXL.cpp b/src/topp/OpenNuXL.cpp index 1c64c970604..dc73c6db48f 100644 --- a/src/topp/OpenNuXL.cpp +++ b/src/topp/OpenNuXL.cpp @@ -37,7 +37,6 @@ #include #include #include -#include #include #include #include @@ -6542,8 +6541,6 @@ static void scoreXLIons_( */ -// NuXLFeatureAugmentation::augment(peptide_ids, positive_weights_features, negative_weights_features); // TODO: seems to work ... scales weights but no improvement - if (RTpredict) { NuXLFDR fdr(1); // 1=keep only top scoring per spectrum @@ -6573,8 +6570,6 @@ static void scoreXLIons_( // write ProteinIdentifications and PeptideIdentifications to IdXML IdXMLFile().store(out_idxml, protein_ids, peptide_ids); -// NuXLFeatureAugmentation::removeAugmented(peptide_ids); // remove augmented features - // generate filtered results #ifdef FILTER_RANKS for (auto & pi : peptide_ids) @@ -6692,8 +6687,6 @@ static void scoreXLIons_( { // load back idXML IdXMLFile().load(perc_out, protein_ids, peptide_ids); - - NuXLFeatureAugmentation::removeAugmented(peptide_ids); // remove augmented features after percolator run // generate filtered results IDFilter::keepNBestHits(peptide_ids, 1); From 29707c77907a2699e47e9b87b4df0a2ca403551a Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 22 Jan 2025 11:59:11 +0100 Subject: [PATCH 318/471] remove some unused functionality --- .../include/OpenMS/ANALYSIS/NUXL/unused.h | 50 ------------------- .../source/ANALYSIS/NUXL/NuXLReport.cpp | 2 +- src/topp/OpenNuXL.cpp | 44 ---------------- 3 files changed, 1 insertion(+), 95 deletions(-) delete mode 100644 src/openms/include/OpenMS/ANALYSIS/NUXL/unused.h diff --git a/src/openms/include/OpenMS/ANALYSIS/NUXL/unused.h b/src/openms/include/OpenMS/ANALYSIS/NUXL/unused.h deleted file mode 100644 index e77f5541bd4..00000000000 --- a/src/openms/include/OpenMS/ANALYSIS/NUXL/unused.h +++ /dev/null @@ -1,50 +0,0 @@ - -//#define ANNOTATED_QUANTILES 1 -#ifdef ANNOTATED_QUANTILES - -#include -#include -using namespace boost::accumulators; - -typedef accumulator_set > quantile_accu_t; -typedef accumulator_set > accumulator_t_quadratic; - -struct SpectrumLevelScoreQuantiles -{ - SpectrumLevelScoreQuantiles(): - acc_(extended_p_square_probabilities = std::vector{ 0.0, 0.25, 0.5, 0.75, 0.9, 0.95, 0.99, 0.999, 0.9999, 0.99999, 1.00 }) - { - } - void insert(double v) { acc_(v); } - - double quantileOfValue(double v) - { - double l = 0.0; - double h = 1.0; - double mid = l + (h - l) / 2.0; // we start with the median (0.5) - double p_value = quantile(acc_, quantile_probability = mid); // value of quantile p - - size_t iter(0); - while (fabs(p_value - v) > 0.01 && iter < 100) - { - mid = l + (h - l) / 2.0; - p_value = quantile(acc_, quantile_probability = mid); // value of quantile p (e.g., 1234.56) - if (p_value > v) // if the current quantile value (e.g., of the median) has a value larger than our value of interest - { - h = mid; // then we need to search in the lower quantile range - } - else - { - l = mid; - } - ++iter; - } - return l; - } - private: - accumulator_t_quadratic acc_; -}; - -#endif - - diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLReport.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLReport.cpp index 3bb4b665f2e..755fc99add8 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLReport.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLReport.cpp @@ -410,7 +410,7 @@ Output format: const std::set proteins = peptide2proteins.at(peptide_sequence_string); const bool is_unique = proteins.size() == 1; - for (const String& acc : proteins) + for (const auto& acc : proteins) { // add basic protein information first time we encounter a protein accession int protein_length{}; diff --git a/src/topp/OpenNuXL.cpp b/src/topp/OpenNuXL.cpp index dc73c6db48f..40e9847259d 100644 --- a/src/topp/OpenNuXL.cpp +++ b/src/topp/OpenNuXL.cpp @@ -102,16 +102,9 @@ //#define DEBUG_OpenNuXL 1 //#define FILTER_BAD_SCORES_ID_TAGS filter out some good hits -//#define FILTER_AMBIGIOUS_PEAKS so far only worse results -//#define FILTER_NO_ARBITRARY_TAG_PRESENT #define CALCULATE_LONGEST_TAG -//#define MODDS_ON_ABY_IONS_ONLY -//#define FILTER_RANKS 1 - #define CONSIDER_AA_LOSSES 1 -#include - using namespace OpenMS; using namespace OpenMS::Internal; using namespace std; @@ -5515,11 +5508,6 @@ static void scoreXLIons_( const Size & scan_index = l->second.first; const PeakSpectrum & exp_spectrum = spectra[scan_index]; - #ifdef FILTER_NO_ARBITRARY_TAG_PRESENT - // require at least one mass tag - if (exp_spectrum.getIntegerDataArrays()[NuXLConstants::IA_DENOVO_TAG_INDEX][0] == 0) { continue; } - #endif - // count candidate for spectrum #ifdef _OPENMP omp_set_lock(&(annotated_peptides_lock[scan_index])); @@ -5722,11 +5710,6 @@ static void scoreXLIons_( ////////////////////////////////////////// // ID-Filter if (skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) { continue; } - -#ifdef FILTER_NO_ARBITRARY_TAG_PRESENT - // require at least one mass tag - if (exp_spectrum.getIntegerDataArrays()[NuXLConstants::IA_DENOVO_TAG_INDEX][0] == 0) { continue; } - #endif #ifdef _OPENMP omp_set_lock(&(annotated_peptides_lock[scan_index])); @@ -5952,11 +5935,6 @@ static void scoreXLIons_( if (precursor_na_adduct != "none" && skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) continue; - -#ifdef FILTER_NO_ARBITRARY_TAG_PRESENT - // require at least one mass tag - if (exp_spectrum.getIntegerDataArrays()[NuXLConstants::IA_DENOVO_TAG_INDEX][0] == 0) { continue; } -#endif #ifdef _OPENMP omp_set_lock(&(annotated_peptides_lock[scan_index])); omp_set_lock(&(annotated_XLs_lock[scan_index])); @@ -6571,29 +6549,7 @@ static void scoreXLIons_( IdXMLFile().store(out_idxml, protein_ids, peptide_ids); // generate filtered results -#ifdef FILTER_RANKS - for (auto & pi : peptide_ids) - { - auto & phs = pi.getHits(); - if (phs.empty()) continue; - if (static_cast(phs[0].getMetaValue("NuXL:isXL")) == 0) continue; // only rerank cross-links - - double max_total_Morph = std::max_element(phs.begin(), phs.end(), - [] (PeptideHit const& lhs, PeptideHit const& rhs) - { - return (double)lhs.getMetaValue("NuXL:total_Morph") < (double)rhs.getMetaValue("NuXL:total_Morph"); - })->getMetaValue("NuXL:total_Morph"); - - auto new_end = std::remove_if(phs.begin(), phs.end(), - [&max_total_Morph](const PeptideHit & ph) - { - return fabs((double)ph.getMetaValue("NuXL:total_Morph") - max_total_Morph) > 1e-4; - }); - phs.erase(new_end, phs.end()); - } -#else IDFilter::keepNBestHits(peptide_ids, 1); -#endif IDFilter::removeUnreferencedProteins(protein_ids, peptide_ids); // split PSMs into XLs and non-XLs but keep only best one of both From b9b9091a077309b9b929b81e7e7213282aea1370 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 22 Jan 2025 12:16:48 +0100 Subject: [PATCH 319/471] Apply suggestions from code review --- .../source/ANALYSIS/ID/FalseDiscoveryRate.cpp | 29 --- .../source/VISUAL/LayerDataBase.cpp | 218 ------------------ 2 files changed, 247 deletions(-) diff --git a/src/openms/source/ANALYSIS/ID/FalseDiscoveryRate.cpp b/src/openms/source/ANALYSIS/ID/FalseDiscoveryRate.cpp index 611152830d9..908ab2c4c9d 100644 --- a/src/openms/source/ANALYSIS/ID/FalseDiscoveryRate.cpp +++ b/src/openms/source/ANALYSIS/ID/FalseDiscoveryRate.cpp @@ -288,35 +288,6 @@ namespace OpenMS // calculate fdr for the forward scores map score_to_fdr; calculateFDRs_(score_to_fdr, target_scores, decoy_scores, q_value, higher_score_better); -/* - TODO: not sure if correct - // make strictly monotonic by interpolating q-values (except for last bin) - auto left = score_to_fdr.begin(); - while (left != score_to_fdr.end()) - { - auto right = left; - ++right; - - // advance right to next q-value - while (right != score_to_fdr.end() && right->second == left->second) - { - ++right; - } - if (right == score_to_fdr.end()) break; // done - - auto start_of_equal_q_values = left; - ++left; // keep first equal q-value the same - size_t steps = std::distance(left, right) + 1; - size_t step = 1; - while (left != right) // start: first q-value with worse score - { - const double q_value_diff = right->second - start_of_equal_q_values->second; - left->second = start_of_equal_q_values->second + (double)step/steps * q_value_diff; - ++left; - } - // now: left == right - } -*/ // calculate peptide FDR if (annotate_peptide_fdr) diff --git a/src/openms_gui/source/VISUAL/LayerDataBase.cpp b/src/openms_gui/source/VISUAL/LayerDataBase.cpp index 44fcf305885..12e6f3726ba 100644 --- a/src/openms_gui/source/VISUAL/LayerDataBase.cpp +++ b/src/openms_gui/source/VISUAL/LayerDataBase.cpp @@ -94,224 +94,6 @@ namespace OpenMS } /* -<<<<<<< HEAD - void LayerDataBase::synchronizePeakAnnotations() - { - // Return if no valid peak layer attached - if (getPeakData() == nullptr || getPeakData()->empty() || type != LayerDataBase::DT_PEAK) - { - return; - } - - // get mutable access to the spectrum - MSSpectrum& spectrum = getPeakDataMuteable()->getSpectrum(current_spectrum_idx_); - - int ms_level = spectrum.getMSLevel(); - - if (ms_level != 2) return; - - // store user fragment annotations - vector& pep_ids = spectrum.getPeptideIdentifications(); - - // no ID selected - if (peptide_id_index == -1 || peptide_hit_index == -1) - { - return; - } - - if (!pep_ids.empty()) - { - vector& hits = pep_ids[peptide_id_index].getHits(); - - if (!hits.empty()) - { - PeptideHit& hit = hits[peptide_hit_index]; - updatePeptideHitAnnotations_(hit); - } - else - {// no hits? add empty hit - PeptideHit hit; - updatePeptideHitAnnotations_(hit); - hits.push_back(hit); - } - } - else// PeptideIdentifications are empty, create new PepIDs and PeptideHits to store the PeakAnnotations - { - // copy user annotations to fragment annotation vector - const Annotations1DContainer& las = getAnnotations(current_spectrum_idx_); - - // no annotations so we don't need to synchronize - bool has_peak_annotation(false); - for (auto& a : las) - { - // only store peak annotations - Annotation1DPeakItem* pa = dynamic_cast(a); - if (pa != nullptr) - { - has_peak_annotation = true; - break; - } - } - if (has_peak_annotation == false) - { - return; - } - PeptideIdentification pep_id; - pep_id.setIdentifier("Unknown"); - - // create a dummy ProteinIdentification for all ID-less PeakAnnotations - vector& prot_ids = getPeakDataMuteable()->getProteinIdentifications(); - if (prot_ids.empty() || prot_ids.back().getIdentifier() != String("Unknown")) - { - ProteinIdentification prot_id; - prot_id.setIdentifier("Unknown"); - prot_ids.push_back(prot_id); - } - - PeptideHit hit; - if (spectrum.getPrecursors().empty() == false) - { - pep_id.setMZ(spectrum.getPrecursors()[0].getMZ()); - hit.setCharge(spectrum.getPrecursors()[0].getCharge()); - } - pep_id.setRT(spectrum.getRT()); - - updatePeptideHitAnnotations_(hit); - std::vector hits; - hits.push_back(hit); - pep_id.setHits(hits); - pep_ids.push_back(pep_id); - } - } - - void LayerDataBase::updatePeptideHitAnnotations_(PeptideHit& hit) - { - // copy user annotations to fragment annotation vector - const Annotations1DContainer& las = getCurrentAnnotations(); - - - const vector& old_fas = hit.getPeakAnnotations(); - - // initialize with an empty vector - vector fas; - - // do not change PeptideHit annotations, if there are no annotations on the spectrum - bool annotations_changed(false); - - // for each annotation item on the canvas - for (auto& a : las) - { - // only store peak annotations (skip general labels and distance annotations) - Annotation1DPeakItem* pa = dynamic_cast(a); - if (pa == nullptr) - { - continue; - } - - auto fa = pa->toPeakAnnotation(); - - // check if peptide hit alread contains the annotation - // Note: we only match by m/z and label. Intensity is ignored to prevent updates from switching - // between relative and absolute mode change the annotation in unpredictable ways. - auto it = std::find_if(old_fas.begin(), old_fas.end(), - [&fa](const PeptideHit::PeakAnnotation& old_fa) { return std::abs(old_fa.mz - fa.mz) < 0.0001 && old_fa.annotation == fa.annotation ;}); - - if (it == old_fas.end()) - { - fas.push_back(fa); - annotations_changed = true; - } - } - - if (annotations_changed) - { - hit.setPeakAnnotations(fas); - } - } - - void LayerDataBase::removePeakAnnotationsFromPeptideHit(const std::vector& selected_annotations) - { - // Return if no valid peak layer attached - if (getPeakData() == nullptr || getPeakData()->empty() || type != LayerDataBase::DT_PEAK) - { - return; - } - - // no ID selected - if (peptide_id_index == -1 || peptide_hit_index == -1) - { - return; - } - - // get mutable access to the spectrum - MSSpectrum& spectrum = getPeakDataMuteable()->getSpectrum(current_spectrum_idx_); - int ms_level = spectrum.getMSLevel(); - - // wrong MS level - if (ms_level < 2) - { - return; - } - - // extract PeptideIdentification and PeptideHit if possible. - // that this function returns prematurely is unlikely, - // since we are deleting existing annotations, - // that have to be somewhere, but better make sure - vector& pep_ids = spectrum.getPeptideIdentifications(); - if (pep_ids.empty()) - { - return; - } - vector& hits = pep_ids[peptide_id_index].getHits(); - if (hits.empty()) - { - return; - } - PeptideHit& hit = hits[peptide_hit_index]; - vector fas = hit.getPeakAnnotations(); - if (fas.empty()) - { - return; - } - - // all requirements fulfilled, PH in hit and annotations in selected_annotations - vector to_remove; - bool annotations_changed(false); - - // collect annotations, that have to be removed - for (auto const& tmp_a : fas) - { - for (auto const& it : selected_annotations) - { - Annotation1DPeakItem* pa = dynamic_cast(it); - // only search for peak annotations - if (pa == nullptr) - { - continue; - } - if (fabs(tmp_a.mz - pa->getPeakPosition()[0]) < 1e-6) - { - if (String(pa->getText()).hasPrefix(tmp_a.annotation)) - { - to_remove.push_back(tmp_a); - annotations_changed = true; - } - } - } - } - // remove the collected annotations from the PeptideHit annotations - for (auto const& tmp_a : to_remove) - { - fas.erase(std::remove(fas.begin(), fas.end(), tmp_a), fas.end()); - } - if (annotations_changed) - { - hit.setPeakAnnotations(fas); - } - } - -======= ->>>>>>> origin/develop */ LayerAnnotatorBase::LayerAnnotatorBase(const FileTypeList& supported_types, const String& file_dialog_text, QWidget* gui_lock) : From 05f76460d6e497e7d7b4c1d2d16fb1d547031e2f Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 22 Jan 2025 13:09:08 +0100 Subject: [PATCH 320/471] add missing include --- src/openms/include/OpenMS/CHEMISTRY/DecoyGenerator.h | 2 ++ src/openms/source/CHEMISTRY/DecoyGenerator.cpp | 2 -- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/openms/include/OpenMS/CHEMISTRY/DecoyGenerator.h b/src/openms/include/OpenMS/CHEMISTRY/DecoyGenerator.h index 16292c1b19d..c0088166a32 100644 --- a/src/openms/include/OpenMS/CHEMISTRY/DecoyGenerator.h +++ b/src/openms/include/OpenMS/CHEMISTRY/DecoyGenerator.h @@ -11,6 +11,8 @@ #include #include +#include + namespace OpenMS { class AASequence; diff --git a/src/openms/source/CHEMISTRY/DecoyGenerator.cpp b/src/openms/source/CHEMISTRY/DecoyGenerator.cpp index 9a453508699..553e55ec636 100644 --- a/src/openms/source/CHEMISTRY/DecoyGenerator.cpp +++ b/src/openms/source/CHEMISTRY/DecoyGenerator.cpp @@ -13,7 +13,6 @@ #include #include -#include using namespace OpenMS; @@ -127,7 +126,6 @@ AASequence DecoyGenerator::shufflePeptides( cached = true; } } - if (cached) return AASequence::fromString(protein_shuffled); String peptide_string_shuffled = peptide_string; From 877f2004ef4bf2e4a12c1e037abfec121740df73 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 22 Jan 2025 14:14:47 +0100 Subject: [PATCH 321/471] missing test files --- src/tests/topp/OpenNuXL_6_output.idXML | 5986 ++++++++++++++++++++++++ src/tests/topp/OpenNuXL_6_output2.tsv | 81 + 2 files changed, 6067 insertions(+) create mode 100644 src/tests/topp/OpenNuXL_6_output.idXML create mode 100644 src/tests/topp/OpenNuXL_6_output2.tsv diff --git a/src/tests/topp/OpenNuXL_6_output.idXML b/src/tests/topp/OpenNuXL_6_output.idXML new file mode 100644 index 00000000000..1069df2befa --- /dev/null +++ b/src/tests/topp/OpenNuXL_6_output.idXML @@ -0,0 +1,5986 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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CountSequenceIsPeptide NuXL:MIC NuXL:pl_pc_MIC NuXL:pl_MIC nr_candidates -ln(poisson) isotope_error A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H fragment_annotation +17.788 712.7828 Cas7 AEADNLDDKK U-H3O4P1 2 66.026290893554688 1 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 226.0590 1343.5841 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 51.069818780383514 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -39.9835 59428.6 1344.5914 672.7993 448.8686 336.9033 112.050621032714844,0.028104400262237,1,"MI:C'"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O"|501.19091796875,0.035030111670494,1,"b5"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O"|584.267578125,9.894491173326969e-03,1,"LDDK+U'"|586.28167724609375,0.011093857698143,1,"a6"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]++ U'-H2O"|599.27777099609375,0.764611601829529,1,"y4+U'-H2O"|606.77734375,0.299497008323669,2,"[M+2H]++ U'-H2O"|614.27984619140625,0.039939478039742,1,"b6"|680.2978515625,0.018134105950594,1,"a6+U'-H2O"|698.31036376953125,6.59028347581625e-03,1,"LDDK+U-H3PO4"|712.36236572265625,0.394213527441025,1,"y5+U'-H2O"|729.31292724609375,6.610926240682602e-03,1,"b7"|795.32373046875,0.023242574185133,1,"a7+U'-H2O"|826.40509033203125,0.400069534778595,1,"y6+U'-H2O"|844.32489013671875,6.451499182730913e-03,1,"b8"|866.3614501953125,0.062791705131531,1,"ADNLDDK+U'-H2O"|884.37408447265625,7.893706671893597e-03,1,"EADNLDDK-H3N1+"|941.43206787109375,0.44364058971405,1,"y7+U'-H2O"|1012.468994140625,0.708723366260529,1,"y8+U'-H2O"|1066.4478759765625,0.035385373979807,1,"b9+U'-H2O"|1141.5120849609375,7.319674827158451e-03,1,"y9+U'-H2O"|1212.5546875,0.066727869212627,1,"[M+H]+ U'-H2O" +17.788 712.7828 Cas7 AEADNLDDKK U-H2O1 2 65.480873107910156 2 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 306.0253 1423.5504 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 51.069818780383514 0 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 51.069818780383514 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 112.050621032714844,0.028104400262237,1,"MI:C'"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O"|501.19091796875,0.035030111670494,1,"b5"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O"|584.267578125,9.894491173326969e-03,1,"LDDK+U'"|586.28167724609375,0.011093857698143,1,"a6"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]++ 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U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O" +18.306 590.7661 Cas6e LDSKGNIK none 2 12.331851959228516 3 0.0 0 LDSKGNIK 873.4920 0.0000 873.4920 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.326696595485117 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -153.0128 349541.2 874.4993 437.7533 292.1713 219.3803 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|147.112808227539063,0.358728766441345,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|431.26043701171875,0.208169266581535,1,"y4" +18.306 590.7661 Cas6e DLYQLHQGLWHLFPNR none 2 8.358111381530762 4 0.0 0 DLYQLHQGLWHLFPNR 2036.0381 0.0000 2036.0381 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.326696595485117 0 0.948040783405304 0.0 0.042552266269922 0.0 0.0 29253 3.119995027343216 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 428.2603 -420264.2 2037.0453 1019.0263 679.6866 510.0168 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|147.112808227539063,0.358728766441345,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|431.26043701171875,0.208169266581535,1,"y4"175.119796752929688,0.014619744382799,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|428.219207763671875,0.510025024414063,2,"LHQGLWH-H3N1++"|484.760772705078125,1.0,2,"LHQGLWHL-H3N1++"|520.25030517578125,0.025870239362121,1,"b4"|794.41949462890625,0.029359607025981,1,"LWHLFP"|855.42803955078125,0.362798720598221,1,"LHQGLWH-H3N1+" +25.116 508.1855 Cas5 YTPYLGR U-H3O4P1 3 30.759143829345703 1 0.637990474700928 0,0.24,0,63.80,0,0,0 YTPyLGR 868.4443 226.0590 1094.5033 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 29.676200157973291 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -142.3438 389085.8 1095.5106 548.2589 365.8417 274.6331 136.0615234375,1.0,1,"MI:A'"|136.07513427734375,0.229426234960556,1,"a1"|152.05633544921875,4.265095572918654e-03,1,"MI:G'"|158.092025756835938,9.572696872055531e-03,1,"y1-H3N1+"|164.070541381835938,3.483457025140524e-03,1,"b1"|175.119049072265625,0.031937755644321,1,"y1"|215.114288330078125,7.323490455746651e-03,1,"y2-H3N1+"|219.112014770507813,7.127284072339535e-03,1,"a2-H2O1+"|232.140228271484375,0.069322824478149,1,"y2"|237.123199462890625,0.195591405034065,1,"a2"|247.107315063476563,2.211090410128236e-03,1,"b2-H2O1+"|265.118011474609375,0.063581943511963,1,"b2"|285.1221923828125,7.153767161071301e-03,1,"PY-CO+C3O"|313.116943359375,3.152150195091963e-03,1,"PY+C3O"|327.1427001953125,1.970470184460282e-03,1,"PY-CO+U'-H2O"|328.198333740234375,2.614108612760902e-03,1,"y3-H3N1+"|329.17095947265625,0.072819426655769,2,"y5+C3O"|345.15252685546875,2.646437846124172e-03,1,"PY-CO+U'"|345.224029541015625,0.10897596180439,1,"y3"|348.06982421875,0.043133333325386,1,"MI:A"|359.1365966796875,2.3593760561198e-03,1,"b2+U'-H2O"|359.186859130859375,0.098186790943146,2,"y5+U'"|373.151611328125,2.350400667637587e-03,1,"PY+U'"|389.189697265625,2.83268908970058e-03,1,"YL+U'"|560.28369140625,0.03523913398385,1,"y4+C3O"|620.31134033203125,0.013985485769808,1,"b5-H2O1+"|657.33489990234375,0.3373843729496,1,"y5+C3O"|717.36590576171875,0.067729890346527,1,"y5+U'"|734.35107421875,3.099862718954682e-03,1,"y4+U-H3PO4"|758.38824462890625,0.013845652341843,1,"y6+C3O"|831.39337158203125,9.685350582003594e-03,1,"y5+U-H3PO4"|903.43212890625,2.896269550547004e-03,1,"[M+H-H2O]+ C3O"|921.44696044921875,0.019729314371943,1,"[M+H]+ C3O" +25.116 508.1855 Cas5 YTPYLGR U-H2O1 3 30.359920501708984 2 0.670666217803955 0,0.24,0,67.07,0,0,0 YTPyLGR 868.4443 306.0253 1174.4696 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 29.676200157973291 0 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 29.676200157973291 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -115.6884 294749.6 1175.4769 588.2421 392.4971 294.6247 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U-H3PO4"|629.2969970703125,1.0,2,"[M+2H]++ U-H3PO4"|642.2138671875,0.065313711762428,1,"b3+U-H3PO4"|669.27935791015625,0.066578842699528,2,"[M+2H+U-H2O1]"|722.1842041015625,0.012603042647243,1,"b3+U-H2O"|735.421142578125,0.030300982296467,1,"y7-H2O1+"|743.26336669921875,0.047368142753839,1,"b4+U-H3PO4"|753.4393310546875,0.262213468551636,1,"y7"|814.327880859375,0.01301802136004,1,"HTVLG+U-H2O"|842.3365478515625,0.057222794741392,1,"b5+U-H3PO4"|898.3970947265625,0.025343561545014,1,"b7+U'"|909.42108154296875,0.010454332455993,1,"b8+C3O"|916.491455078125,0.011721312068403,1,"y8"|927.43896484375,0.037982285022736,1,"a6+U-H3PO4"|955.418212890625,0.050513833761215,1,"b6+U-H3PO4"|1031.5264892578125,0.180062636733055,1,"[M+H]+"|1083.4879150390625,0.025055043399334,1,"b8+U-H3PO4"|1143.546875,0.033915352076292,1,"[M+H]+ U'" +26.237 678.2844 Cas5 DYHTVLGAR U-H3O4P1 2 61.233551025390625 2 0.822381615638733 0,82.24,0,0,21.96,0,0,0,0 DyHTVLGAR 1030.5196 226.0590 1256.5786 12.389053344726563 10.107473373413086 1 1 1 0 0.218422010540962 4.155429840087891 0.046298556029797 29253 29.580006293714821 0 12.389053344726563 10.107473373413086 1 1 1 0 0.218422010540962 3.148078680038452 0.046298556029797 29253 29.580006293714821 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 -48.9879 77845.4 1257.5858 629.2966 419.8668 315.1519 110.071525573730469,0.124598376452923,1,"iH+"|112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|204.134170532226563,0.047920491546392,1,"y2-C1H2N2+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|229.127822875976563,6.706117186695337e-03,1,"y2-H3N1+"|239.113800048828125,7.95002281665802e-03,1,"HT"|246.155319213867188,0.029895069077611,1,"y2"|286.150421142578125,0.037254326045513,1,"y3-H3N1+"|303.177154541015625,0.322829812765121,1,"y3"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|368.21673583984375,0.152305349707603,2,"y7-H2O1++"|377.221343994140625,0.194865599274635,2,"y7"|399.233306884765625,0.032629072666168,1,"y4-H3N1+"|415.200531005859375,0.011067586950958,1,"y3+U'"|416.16107177734375,9.909789077937603e-03,1,"b3"|416.2611083984375,0.390764862298965,1,"y4"|423.222259521484375,0.047973766922951,1,"TVLG+C3O"|477.163330078125,0.041644386947155,1,"a2+U-H3PO4"|499.19189453125,8.276323787868023e-03,1,"b4-H2O1+"|505.15753173828125,0.058943208307028,1,"b2+U-H3PO4"|510.177032470703125,9.497386403381825e-03,1,"b3+U'-H2O"|515.33038330078125,0.247247070074081,1,"y5"|517.205078125,0.010058866813779,1,"b4"|527.185791015625,0.053621523082256,1,"YH+U-H3PO4"|571.7821044921875,0.309090524911881,2,"y8+U-H3PO4"|598.37109375,0.028361488133669,1,"y6-H2O1+"|614.22186279296875,0.011790351010859,1,"a3+U-H3PO4"|616.3775634765625,0.524602711200714,1,"y6"|620.29071044921875,0.307169079780579,2,"[M+2H-H2O]++ 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0.218422010540962 3.148078680038452 0.046298556029797 29253 29.580006293714821 0 12.389053344726563 0.0 1 1 1 0 0.218422010540962 0.0 0.0 29253 18.310972718725807 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 -162.0173 313824.7 1031.5269 516.2671 344.5138 258.6372 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+26.413 791.8590 Cse2 KSEQTTGISLGR U-H2O1 2 55.023689270019531 2 0.718522191047669 71.85,28.95,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 75.34557345389112 0 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 75.34557345389112 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 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U'-H2O"|685.85467529296875,1.0,2,"[M+2H]++ U'-H2O"|703.409912109375,0.085564941167831,1,"y7"|759.3389892578125,3.510346170514822e-03,1,"SEQTTGIS-CO-H3N1+"|769.3367919921875,3.813720541074872e-03,1,"SEQTTGI+C3O"|785.39312744140625,2.953411778435111e-03,1,"EQTTGISL-CO-H3N1+"|786.44580078125,3.075511427596211e-03,1,"y8-H2O1+"|804.4573974609375,0.129444718360901,1,"y8"|826.368896484375,7.392823696136475e-03,1,"b7+U'-H2O"|872.4322509765625,3.032000968232751e-03,1,"SEQTTGISL-CO-H3N1+"|873.38275146484375,8.629622869193554e-03,1,"a6+U-H3PO4"|911.447265625,9.337763302028179e-03,1,"EQTTGISLG-CO+C3O"|915.49517822265625,0.018657565116882,1,"y9-H3N1+"|932.51495361328125,0.120762772858143,1,"y9"|939.470703125,0.02140568383038,1,"b8+U'-H2O"|979.41162109375,9.381845593452454e-03,1,"QTTGISL-CO+U-H2O"|1026.4990234375,0.016941957175732,1,"b9+U'-H2O"|1043.5543212890625,0.036094401031733,1,"y10-H2O1+"|1045.54541015625,7.805424276739359e-03,1,"b10"|1061.558349609375,0.197863757610321,1,"y10"|1130.56640625,0.0313437320292,1,"y11-H2O1+"|1148.594970703125,0.08852231502533,1,"y11"|1158.5897216796875,0.020451299846172,1,"y9+U-H3PO4" +26.413 791.8590 Cse2 KSEQTTGISLGR none 2 31.117559432983398 3 0.0 0 KSEQTTGISLGR 1275.6783 0.0000 1275.6783 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 75.34557345389112 0 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 75.34557345389112 0 19.087356567382813 0.0 1 1 1 0 0.221869960427284 0.0 0.0 29253 50.441228020739317 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 -153.0126 239513.9 1276.6856 638.8464 426.2334 319.9268 112.050689697265625,9.990843944251537e-03,1,"MI:C'"|129.102371215820313,0.013408292084932,1,"b1"|136.061798095703125,0.902763903141022,1,"MI:A'"|136.074905395507813,0.051667388528585,1,"iK(C5H10N1)C3O"|152.056564331054688,3.377486718818545e-03,1,"MI:G'"|158.092697143554688,0.024075241759419,1,"y1-H3N1+"|175.118927001953125,0.081427209079266,1,"y1"|178.097412109375,0.341100573539734,1,"iK(C5H10N1)U'-H2O"|195.123382568359375,0.017177894711494,1,"a1+U'-H2O"|215.113723754882813,0.014229998923838,1,"y2-H3N1+"|227.066909790039063,0.016493165865541,1,"MI:U-H3PO4"|232.140274047851563,0.180095225572586,1,"y2"|241.1295166015625,0.01908091455698,1,"b1+U'"|258.143798828125,3.849325468763709e-03,1,"GIS"|282.156463623046875,0.019274268299341,1,"a2+U'-H2O"|310.150787353515625,0.118582129478455,1,"b2+U'-H2O"|327.212188720703125,3.42642655596137e-03,1,"y3-H2O1+"|328.199676513671875,4.501644056290388e-03,1,"y3-H3N1+"|345.223907470703125,0.247861370444298,1,"y3"|348.0692138671875,7.973242551088333e-03,1,"MI:A"|428.180908203125,8.386147208511829e-03,1,"SEQT-H2O1+"|432.25604248046875,0.183289110660553,1,"y4"|439.19366455078125,0.044542569667101,1,"b3+U'-H2O"|517.22088623046875,3.666676813736558e-03,1,"EQTTG"|529.219970703125,9.659912437200546e-03,1,"SEQTT-H2O1+"|545.3385009765625,0.023281643167138,1,"TTGISL-CO"|567.25286865234375,0.052726376801729,1,"b4+U'-H2O"|602.3612060546875,0.080439247190952,1,"TTGISLG-CO"|676.849365234375,0.461511492729187,2,"[M+2H-H2O]++ 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112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" +33.237 510.2805 Cas7 LLKVLK none 2 13.002236366271973 3 0.0 0 LLKVLK 712.5211 0.0000 712.5211 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 18.84328919765186 0 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 18.84328919765186 0 2.676236867904663 0.0 1 1 1 0 0.182740524411201 0.0 0.0 29253 7.21665132770771 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -153.0127 428285.7 713.5284 357.2678 238.5143 179.1376 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3" +33.237 510.2805 Cas7 KLLKVLK none 2 12.645284652709961 4 0.0 0 KLLKVLK 840.6161 0.0000 840.6161 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 18.84328919765186 0 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 18.84328919765186 0 2.676236867904663 0.0 1 1 1 0 0.182740524411201 0.0 0.0 29253 7.21665132770771 0 3.208958625793457 0.0 0.136603727936745 0.0 0.0 29253 8.896032099035239 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -88.9652 211160.6 841.6233 421.3153 281.2126 211.1613 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"LL-CO"|227.175506591796875,0.098765894770622,1,"LL"|242.18536376953125,0.01018890645355,1,"b2"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3" +33.791 717.3553 Cas7 VLKEDIAAIR U-H3O4P1 2 30.723300933837891 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 226.0590 1352.7300 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -39.9831 59026.7 1353.7373 677.3723 451.9173 339.1898 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" +33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 30.485282897949219 2 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" +33.791 717.3553 Cas7 EDIAAIR none 2 20.511859893798828 3 0.0 0 EDIAAIR 786.4236 0.0000 786.4236 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 7.072373390197754 0.0 0.099335506558418 0.0 0.0 29253 13.981020318661976 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -323.1363 819687.1 787.4308 394.2191 263.1485 197.6132 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"130.049942016601563,0.014329176396132,1,"b1"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|543.36065673828125,0.106723681092262,1,"y5"|658.3885498046875,0.117386691272259,1,"y6" +33.791 717.3553 Cas7 VLKEDIAAIR none 2 19.036767959594727 4 0.0 0 VLKEDIAAIR 1126.6710 0.0000 1126.6710 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 7.072373390197754 0.0 0.099335506558418 0.0 0.0 29253 13.981020318661976 0 9.227341651916504 0.0 1 1 1 0 0.158668205142021 0.0 0.0 29253 15.783117699886407 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -153.0126 271134.1 1127.6783 564.3428 376.5643 282.6750 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ 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1.844556570053101 184.46,126.75,97.82,0,0,32.15,32.15,0,0,0,0,0 mATSGMMTELGK 1255.5611 226.0590 1481.6200 19.278144836425781 14.91402530670166 1 1 1 0 0.371337056159973 4.102765560150146 0.158967092633247 29253 54.593068364401354 0 5.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -48.9889 66039.0 1482.6273 741.8173 494.8806 371.4123 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H2O1+"|953.44305419921875,0.880237638950348,1,"y9"|1036.4752197265625,0.154976740479469,1,"y10-H2O1+"|1037.4661865234375,0.044277537614107,1,"y10-H3N1+"|1054.489013671875,0.891642868518829,1,"y10"|1107.508056640625,0.010800593532622,1,"y11-H2O1+"|1125.5260009765625,0.135128006339073,1,"y11" +34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U-H2O1 2 32.330818176269531 1 0.536135375499725 0,0,0,53.61,0,0,0,0,6.09 MVFcLSAGK 970.4616 306.0253 1276.4869 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -9.0052 14087.1 1277.4942 639.2507 426.5029 320.1290 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O" +34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK UU-H2O1 2 31.977167129516602 2 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 612.0506 1582.5122 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 144.0075 -181767.2 1583.5195 792.2634 528.5114 396.6353 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U" +34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK none 2 21.468671798706055 3 0.0 0 MVFCLSAGK 970.4616 0.0000 970.4616 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 9.10000755455453 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -162.0178 333206.8 971.4689 486.2381 324.4945 243.6227 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U"120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|147.112640380859375,0.216315641999245,1,"y1"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5" +34.072 648.2559 Cse2 HQQALLRMVFCLSAGK none 2 16.85017204284668 4 0.0 0 HQQALLRMVFCLSAGK 1800.9491 0.0000 1800.9491 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 9.10000755455453 0 5.535978317260742 0.0 0.133406266570091 0.0 0.0 29253 7.792995663845979 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 253.2259 -280899.6 1801.9564 901.4818 601.3237 451.2446 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+36.767 933.9406 Cas7 TLALLSGKSVDEAEK U-H3O4P1 2 38.031223297119141 1 0.146051496267319 0,0,0,0,0,0,0,14.61,0,0,0,0,0,0,14.61 TLALLSGkSVDEAEk 1559.8407 226.0590 1785.8996 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 24.284693983617309 0 100.00 19.27 98.86 2.97 4.81 0.00 0.00 0.00 -39.9835 44726.4 1786.9069 893.9571 596.3072 447.4822 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ 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-0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ 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U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" +39.118 623.2540 Cse2 MLTWWGK UU-H3O4P1 2 36.48870849609375 2 1.08866548538208 0,0.95,0,108.87,16.34,0,7.64 MLTwWGK 920.4578 532.0843 1452.5421 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 10.942926113371858 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 10.942926113371858 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 104.0244 -143032.4 1453.5494 727.2783 485.1880 364.1428 112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U"112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" +39.118 623.2540 Cas6e VPLIKEAEQIAWLQR none 2 17.291851043701172 3 0.0 0 VPLIKEAEQIAWLQR 1793.0200 0.0000 1793.0200 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 10.942926113371858 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 10.942926113371858 0 4.992705345153809 0.0 0.040718141943216 0.0 0.0 29253 10.942926113371858 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 274.2633 -305580.0 1794.0272 897.5173 598.6806 449.2623 112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U"112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ 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From a413358b6526bf9955c55950a45d37ebf7934e9b Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 22 Jan 2025 16:43:34 +0100 Subject: [PATCH 322/471] partial loss score still different --- src/topp/OpenNuXL.cpp | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/topp/OpenNuXL.cpp b/src/topp/OpenNuXL.cpp index 40e9847259d..74ffb901eeb 100644 --- a/src/topp/OpenNuXL.cpp +++ b/src/topp/OpenNuXL.cpp @@ -1178,11 +1178,12 @@ class OpenNuXL : static double logfactorial_(UInt x) { + const double dx = static_cast(x); if (x < 2) { return 0; } double z(0); - for (double y = 2; y <= static_cast(x); ++y) { z += log(static_cast(y)); } - return z; - } + for (double y = 2; y <= dx; ++y) { z += std::log(y); } + return z; + } // score ions without nucleotide shift static void scorePeptideIons_( @@ -1430,7 +1431,7 @@ class OpenNuXL : const double bFact = logfactorial_(b_ion_count); const double aFact = logfactorial_(a_ion_count); const double yFact = logfactorial_(y_ion_count); - hyperScore = log1p(dot_product) + yFact + bFact + aFact; + hyperScore = std::log1p(dot_product) + yFact + bFact + aFact; MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum MIC /= TIC; @@ -1984,7 +1985,7 @@ class OpenNuXL : const double bFact = logfactorial_(b_ion_count); const double aFact = logfactorial_(a_ion_count); const double yFact = logfactorial_(y_ion_count); - plss_hyperScore = log1p(dot_product) + yFact + bFact + aFact; + plss_hyperScore = std::log1p(dot_product) + yFact + bFact + aFact; plss_MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum plss_MIC /= TIC; From 0830d4e3eb12ed3a39c6b1c4503b515598ce838a Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 22 Jan 2025 16:43:34 +0100 Subject: [PATCH 323/471] partial loss score still different --- src/topp/OpenNuXL.cpp | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/src/topp/OpenNuXL.cpp b/src/topp/OpenNuXL.cpp index 40e9847259d..98bfdfa1acb 100644 --- a/src/topp/OpenNuXL.cpp +++ b/src/topp/OpenNuXL.cpp @@ -82,10 +82,6 @@ #include #include -#include -#include -#include - #include #include @@ -93,6 +89,12 @@ #include +#include +#include +#include +#include + + #ifdef _OPENMP #include #define NUMBER_OF_THREADS (omp_get_num_threads()) @@ -1178,11 +1180,12 @@ class OpenNuXL : static double logfactorial_(UInt x) { + const double dx = static_cast(x); if (x < 2) { return 0; } double z(0); - for (double y = 2; y <= static_cast(x); ++y) { z += log(static_cast(y)); } - return z; - } + for (double y = 2; y <= dx; ++y) { z += std::log(y); } + return z; + } // score ions without nucleotide shift static void scorePeptideIons_( @@ -1430,7 +1433,7 @@ class OpenNuXL : const double bFact = logfactorial_(b_ion_count); const double aFact = logfactorial_(a_ion_count); const double yFact = logfactorial_(y_ion_count); - hyperScore = log1p(dot_product) + yFact + bFact + aFact; + hyperScore = std::log1p(dot_product) + yFact + bFact + aFact; MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum MIC /= TIC; @@ -1984,7 +1987,7 @@ class OpenNuXL : const double bFact = logfactorial_(b_ion_count); const double aFact = logfactorial_(a_ion_count); const double yFact = logfactorial_(y_ion_count); - plss_hyperScore = log1p(dot_product) + yFact + bFact + aFact; + plss_hyperScore = std::log1p(dot_product) + yFact + bFact + aFact; plss_MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum plss_MIC /= TIC; From 7ab5ee2f8762ef555d22653f9181d6362356799f Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Wed, 22 Jan 2025 17:41:01 +0100 Subject: [PATCH 324/471] removed some compile warnings --- src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp | 2 +- src/tests/topp/OpenNuXL_1_output.idXML | 122 ++--- src/tests/topp/OpenNuXL_2_output.idXML | 122 ++--- src/tests/topp/OpenNuXL_3_output.idXML | 458 +++++-------------- src/tests/topp/OpenNuXL_3_output2.tsv | 7 +- src/tests/topp/OpenNuXL_4_output.idXML | 318 ++++--------- src/tests/topp/OpenNuXL_4_output2.tsv | 4 +- src/tests/topp/OpenNuXL_5_output.idXML | 122 ++--- src/tests/topp/OpenNuXL_6_output.idXML | 470 ++++++++++---------- src/tests/topp/OpenNuXL_6_output2.tsv | 160 +++---- src/topp/OpenNuXL.cpp | 23 +- 11 files changed, 714 insertions(+), 1094 deletions(-) diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp index f510c76d8ca..2b5309e84cb 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp @@ -230,7 +230,7 @@ namespace OpenMS { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "q-value list for PSMs and peptides differ in size.", - String(xl_PSM_qvalue_thresholds.size() + "!=" + String(xl_peptidelevel_qvalue_thresholds.size()))); + String(xl_PSM_qvalue_thresholds.size()) + "!=" + String(xl_peptidelevel_qvalue_thresholds.size())); } for (Size i = 0; i != xl_PSM_qvalue_thresholds.size(); ++i) diff --git a/src/tests/topp/OpenNuXL_1_output.idXML b/src/tests/topp/OpenNuXL_1_output.idXML index 9e05f36bc75..b925a3fc4e6 100644 --- a/src/tests/topp/OpenNuXL_1_output.idXML +++ b/src/tests/topp/OpenNuXL_1_output.idXML @@ -6,7 +6,7 @@ - + @@ -49,7 +49,7 @@ - + @@ -57,7 +57,7 @@ - + @@ -78,7 +78,7 @@ - + @@ -129,7 +129,7 @@ - + @@ -137,7 +137,7 @@ - + @@ -158,7 +158,7 @@ - + @@ -209,7 +209,7 @@ - + @@ -217,7 +217,7 @@ - + @@ -238,7 +238,7 @@ - + @@ -289,7 +289,7 @@ - + @@ -297,7 +297,7 @@ - + @@ -318,7 +318,7 @@ - + @@ -369,7 +369,7 @@ - + @@ -377,7 +377,7 @@ - + @@ -398,7 +398,7 @@ - + @@ -449,7 +449,7 @@ - + @@ -457,7 +457,7 @@ - + @@ -478,7 +478,7 @@ - + @@ -529,7 +529,7 @@ - + @@ -537,7 +537,7 @@ - + @@ -558,7 +558,7 @@ - + @@ -609,7 +609,7 @@ - + @@ -617,7 +617,7 @@ - + @@ -638,7 +638,7 @@ - + @@ -689,7 +689,7 @@ - + @@ -697,7 +697,7 @@ - + @@ -718,7 +718,7 @@ - + @@ -769,7 +769,7 @@ - + @@ -777,7 +777,7 @@ - + @@ -798,7 +798,7 @@ - + @@ -849,7 +849,7 @@ - + @@ -857,7 +857,7 @@ - + @@ -878,7 +878,7 @@ - + @@ -929,7 +929,7 @@ - + @@ -937,7 +937,7 @@ - + @@ -958,7 +958,7 @@ - + @@ -1009,7 +1009,7 @@ - + @@ -1017,7 +1017,7 @@ - + @@ -1038,7 +1038,7 @@ - + @@ -1089,7 +1089,7 @@ - + @@ -1097,7 +1097,7 @@ - + @@ -1118,7 +1118,7 @@ - + @@ -1169,7 +1169,7 @@ - + @@ -1177,7 +1177,7 @@ - + @@ -1198,7 +1198,7 @@ - + @@ -1249,7 +1249,7 @@ - + @@ -1257,7 +1257,7 @@ - + @@ -1278,7 +1278,7 @@ - + @@ -1329,7 +1329,7 @@ - + @@ -1337,7 +1337,7 @@ - + @@ -1358,7 +1358,7 @@ - + @@ -1409,7 +1409,7 @@ - + @@ -1417,7 +1417,7 @@ - + @@ -1438,7 +1438,7 @@ - + @@ -1489,7 +1489,7 @@ - + @@ -1497,7 +1497,7 @@ - + @@ -1518,7 +1518,7 @@ - + @@ -1569,7 +1569,7 @@ - + @@ -1577,7 +1577,7 @@ - + @@ -1598,7 +1598,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_2_output.idXML b/src/tests/topp/OpenNuXL_2_output.idXML index ef722170577..adfd69aea78 100644 --- a/src/tests/topp/OpenNuXL_2_output.idXML +++ b/src/tests/topp/OpenNuXL_2_output.idXML @@ -6,7 +6,7 @@ - + @@ -49,7 +49,7 @@ - + @@ -57,7 +57,7 @@ - + @@ -78,7 +78,7 @@ - + @@ -129,7 +129,7 @@ - + @@ -137,7 +137,7 @@ - + @@ -158,7 +158,7 @@ - + @@ -209,7 +209,7 @@ - + @@ -217,7 +217,7 @@ - + @@ -238,7 +238,7 @@ - + @@ -289,7 +289,7 @@ - + @@ -297,7 +297,7 @@ - + @@ -318,7 +318,7 @@ - + @@ -369,7 +369,7 @@ - + @@ -377,7 +377,7 @@ - + @@ -398,7 +398,7 @@ - + @@ -449,7 +449,7 @@ - + @@ -457,7 +457,7 @@ - + @@ -478,7 +478,7 @@ - + @@ -529,7 +529,7 @@ - + @@ -537,7 +537,7 @@ - + @@ -558,7 +558,7 @@ - + @@ -609,7 +609,7 @@ - + @@ -617,7 +617,7 @@ - + @@ -638,7 +638,7 @@ - + @@ -689,7 +689,7 @@ - + @@ -697,7 +697,7 @@ - + @@ -718,7 +718,7 @@ - + @@ -769,7 +769,7 @@ - + @@ -777,7 +777,7 @@ - + @@ -798,7 +798,7 @@ - + @@ -849,7 +849,7 @@ - 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+61,7 @@ - + @@ -69,7 +69,7 @@ - + @@ -141,7 +141,7 @@ - + @@ -149,7 +149,7 @@ - + @@ -221,7 +221,7 @@ - + @@ -229,7 +229,7 @@ - + @@ -301,7 +301,7 @@ - + @@ -309,7 +309,7 @@ - + @@ -359,78 +359,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -453,7 +381,7 @@ - + @@ -461,7 +389,7 @@ - + @@ -533,7 +461,7 @@ - + @@ -541,7 +469,7 @@ - + @@ -609,7 +537,7 @@ - + @@ -617,7 +545,7 @@ - + @@ -685,7 +613,7 @@ - + @@ -693,7 +621,7 @@ - + @@ -761,7 +689,7 @@ - + @@ -769,7 +697,7 @@ - + @@ -837,7 +765,7 @@ - + @@ -845,7 +773,7 @@ - + @@ -895,47 +823,47 @@ - - + + - - + + - + - - + + - - - - + + + + - + - - + + - - + + - - + + - + - - - + + + @@ -946,17 +874,13 @@ - - - + + + - - - - - - + + @@ -965,54 +889,54 @@ - - - - - + + + + + - - + + - + - + - - - - + + + + - - - - - - + + + + + + - - + + - - + + - - + + - + - - - - + + + + @@ -1022,13 +946,17 @@ - - - - + + + + - - + + + + + + @@ -1037,11 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- - - - - - - - - - - - - - - - - - - - @@ -2233,7 +2017,7 @@ - + @@ -2241,7 +2025,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_3_output2.tsv b/src/tests/topp/OpenNuXL_3_output2.tsv index 958aa70fd29..d3aa37d250b 100644 --- a/src/tests/topp/OpenNuXL_3_output2.tsv +++ b/src/tests/topp/OpenNuXL_3_output2.tsv @@ -3,15 +3,14 @@ 18.306 590.7661 Cas6e LDSKGNIK U-H2O1 2 25.741664886474609 1 2.196093797683716 0,0,0,219.61,0,0,0,8.00 LDSkGNIK 873.4920 306.0253 1179.5173 2.428377628326416 4.320775508880615 1 1 1 0 0.130456954240799 0.0 0.175812318921089 1 315.0 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 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28.487 828.6961 Cas6e VEDVHPISERPQYFSGDGK U 3 49.829761505126953 1 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 VEDVHPISERPQYFSGDGK 2159.0284 324.0359 2483.0642 14.357150077819824 9.840764999389649 1 1 1 0 0.205655053257942 0.0 0.291826844215393 2 315.0 0 27.36 6.64 0.96 0.00 0.70 0.00 0.00 0.00 -0.0008 0.9 2484.0715 1242.5394 828.6954 621.7733 110.071479797363281,0.362966805696487,1,"iH+"|112.050910949707031,9.644773788750172e-03,1,"MI:C'"|129.102279663085938,0.166269198060036,1,"y1-H2O1+"|130.086685180664063,0.045289572328329,1,"y1-H3N1+"|136.061782836914063,0.273647636175156,1,"MI:A'"|147.112640380859375,0.066893331706524,1,"y1"|152.055984497070313,6.967935245484114e-03,1,"MI:G'"|183.111434936523438,5.116867832839489e-03,1,"a2-H2O1+"|183.148483276367188,0.036467146128416,1,"PI-CO"|186.123275756835938,0.077058076858521,1,"y2-H2O1+"|187.107864379882813,0.053842004388571,1,"DV-CO"|201.123031616210938,0.125200733542442,1,"IS"|204.134048461914063,0.550349652767181,1,"y2"|209.13958740234375,0.034710466861725,1,"VH-CO"|211.143310546875,0.025080092251301,1,"PI"|227.06475830078125,5.420028697699308e-03,1,"ED-H2O1+"|229.11810302734375,0.129732340574265,1,"b2"|235.118820190429688,0.057845514267683,1,"HP"|237.1348876953125,0.129707276821136,1,"VH"|245.076187133789063,0.020547781139612,1,"ED"|257.092529296875,0.010260656476021,1,"SG+U'"|274.118988037109375,0.017112335190177,1,"FSG-H2O1+"|319.160888671875,0.035657577216625,1,"y3"|326.134033203125,8.992774412035942e-03,1,"b3-H2O1+"|344.14459228515625,0.385335296392441,1,"b3"|352.160003662109375,0.088167294859886,1,"DVH"|376.181060791015625,0.054880749434233,1,"y4"|399.231170654296875,0.013289213180542,1,"PISE-CO"|415.21783447265625,0.089179709553719,1,"a4"|435.199798583984375,7.126581389456987e-03,1,"EDVH-CO-H2O1+"|436.184295654296875,0.041907016187906,1,"FSGDG-CO"|443.2122802734375,0.054962232708931,1,"b4"|445.204132080078125,9.107047691941261e-03,1,"y5-H2O1+"|453.210479736328125,7.662034593522549e-03,1,"EDVH-CO"|463.213165283203125,0.057442601770163,1,"y5"|481.20404052734375,0.064231678843498,1,"EDVH"|509.202301025390625,0.035260323435068,1,"YF-CO+U-H3PO4"|534.26385498046875,9.28904116153717e-03,1,"a5-H2O1+"|552.27685546875,0.323687613010407,1,"a5"|562.2611083984375,0.010503350757062,1,"b5-H2O1+"|580.27117919921875,0.412556946277618,1,"b5"|583.3218994140625,0.049311552196741,1,"ISERP"|648.6285400390625,0.104770556092262,3,"y15+U-H3PO4"|675.2918701171875,0.020023381337523,3,"y15+U-H2O"|677.32470703125,0.019785417243838,1,"b6"|681.2958984375,0.047548152506351,3,"y15+U"|719.99578857421875,0.057050332427025,3,"y17+U-H3PO4"|738.01220703125,0.044156819581985,3,"a18+U-H3PO4"|741.83135986328125,0.020303577184677,2,"y12+U'"|758.01837158203125,0.13004507124424,3,"[M+3H]+++ 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U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"b4+C3O"|548.35498046875,0.371608823537827,1,"KLLV+U'-H2O"|562.3695068359375,0.036407515406609,1,"b4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" 33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 31.678943634033203 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 0.0 0.059569962322712 2 315.0 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" @@ -23,8 +22,6 @@ 37.536 833.8672 Cse2 LVQPFGWENPR U 2 52.818855285644531 1 5.590284824371338 8.97,0,0,0,0,0,559.03,0,0,0,0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 5.432636737823486 5.498913288116455 1 1 1 0 0.222448781132698 0.0 0.252318680286407 1 315.0 0 47.85 8.60 8.42 0.00 4.17 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 112.050765991210938,0.08420105278492,1,"MI:C'"|120.080955505371094,0.248142316937447,1,"iF+"|136.061904907226563,0.478474080562592,1,"MI:A'"|152.056915283203125,0.041747037321329,1,"MI:G'"|158.092987060546875,0.02823868393898,1,"y1-H3N1+"|175.118865966796875,0.431510150432587,1,"y1"|185.164825439453125,0.975687205791473,1,"a2"|205.096786499023438,0.015142207033932,1,"FG"|208.107650756835938,0.072737187147141,1,"b1+U'-H2O"|213.159622192382813,0.55321729183197,1,"b2"|217.133560180664063,0.150055125355721,1,"PF-CO"|228.134170532226563,0.134030729532242,1,"VQ"|245.128326416015625,0.073948614299297,1,"PF"|255.145156860351563,0.044952541589737,1,"y2-H3N1+"|268.1070556640625,0.017682727426291,1,"GW-CO+C3O"|271.1207275390625,0.015898240730166,1,"FG-CO+U'-H2O"|272.17138671875,0.733417451381683,1,"y2"|302.1507568359375,0.017543597146869,1,"PFG"|323.207000732421875,0.023342134431005,1,"b3-H2O1+"|341.217620849609375,0.281899809837341,1,"b3"|368.202545166015625,0.018031865358353,1,"y3-H2O1+"|369.186676025390625,0.024854462593794,1,"y3-H3N1+"|373.18609619140625,0.037409465759993,1,"QPF"|384.165252685546875,0.020501535385847,1,"WEN-CO-H2O1+"|386.214569091796875,0.333306282758713,1,"y3"|465.113739013671875,0.085212588310242,1,"iW+U-H2O"|483.124237060546875,0.077979676425457,1,"FG-CO+U-H2O"|497.247100830078125,0.052800357341766,1,"y4-H2O1+"|515.25689697265625,0.456620991230011,1,"y4"|522.14117431640625,0.024717634543777,1,"GW-CO+U-H2O"|557.75213623046875,0.042095232754946,2,"y8+U'"|566.24700927734375,0.018172480165958,1,"GWENP-H2O1+"|612.78509521484375,0.067495785653591,2,"y9+U'-H2O"|614.77642822265625,0.18346481025219,2,"y8+U-H3PO4"|654.75494384765625,0.182821094989777,2,"y8+U-H2O"|663.76007080078125,0.391415536403656,2,"y8+U"|678.8104248046875,0.125872269272804,2,"y9+U-H3PO4"|697.19720458984375,0.01831066608429,1,"GWE+U"|718.7857666015625,0.509350657463074,2,"y9+U-H2O"|870.38726806640625,0.020341049879789,1,"y6+U'"|909.38018798828125,0.016918642446399,1,"b5+U"|941.30230712890625,0.016845868900418,1,"PFGWE+U"|984.421630859375,0.171274989843369,1,"y6+U-H3PO4"|1002.4327392578125,0.077881030738354,1,"y6+U-HPO3"|1007.3658447265625,0.02186157181859,1,"y5+U-H2O"|1017.45574951171875,0.016997389495373,1,"y7+U'"|1025.3704833984375,0.067600704729557,1,"y5+U"|1037.34326171875,0.015292263589799,1,"PFGWEN+U-H2O"|1064.37841796875,0.220285996794701,1,"y6+U-H2O"|1082.393310546875,0.415275424718857,1,"y6+U"|1114.5091552734375,0.116430044174194,1,"y8+U'"|1131.4898681640625,0.07273530960083,1,"y7+U-H3PO4"|1149.4764404296875,0.018299410119653,1,"y7+U-HPO3"|1154.4898681640625,0.135885670781136,1,"QPFGWENP-CO+U-H3PO4"|1211.4739990234375,0.09792023897171,1,"y7+U-H2O"|1228.5391845703125,0.487874060869217,1,"y8+U-H3PO4"|1246.5452880859375,0.41549888253212,1,"y8+U-HPO3"|1308.5025634765625,0.782280921936035,1,"y8+U-H2O"|1326.51611328125,1.0,1,"y8+U" 37.864 698.2974 Cas5 DEPMITLPR U 2 67.925018310546875 1 0.827892243862152 0,0,82.79,0,0,0,0,12.18,0 DEpMITLPR 1070.5430 324.0359 1394.5789 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 112.050773620605469,0.042819745838642,1,"MI:C'"|136.061843872070313,0.196844235062599,1,"MI:A'"|152.056671142578125,0.023113740608096,1,"MI:G'"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1"|182.092300415039063,0.052632980048656,1,"iP+U'"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2"|253.100723266601563,9.467311203479767e-03,1,"PM-CO+C3O"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2"|281.09564208984375,9.001040831208229e-03,1,"PM+C3O"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|313.13702392578125,0.016673086211085,1,"PM-CO+U'"|341.126983642578125,0.080299213528633,1,"PM+U'"|348.068084716796875,9.060680866241455e-03,1,"MI:A"|376.089996337890625,0.029012143611908,1,"iP+U-H2O"|385.25506591796875,0.261529922485352,1,"y3"|394.095611572265625,0.040202785283327,1,"iP+U"|426.217559814453125,7.179270498454571e-03,1,"PMI-CO+U'"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O"|454.151214599609375,0.077750355005264,1,"b3+U'"|454.217010498046875,7.962716743350029e-03,1,"PMI+U'"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4"|525.14324951171875,0.028857138007879,1,"PM-CO+U"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"PM+U-H2O"|537.2529296875,9.177219122648239e-03,1,"PMIT+U'-H2O"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|553.13372802734375,0.032937977463007,1,"PM+U"|553.27215576171875,0.012286836281419,1,"MITL+U'-H2O"|555.264404296875,9.468427859246731e-03,1,"PMIT+U'"|567.26251220703125,0.116328254342079,2,"y7+U-H2O"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U"|585.19580078125,8.00114031881094e-03,1,"b4+U'"|599.387451171875,0.483213186264038,1,"y5"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]++ U-H3PO4"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O"|649.3082275390625,0.248698011040688,2,"[M+2H]++ U-H3PO4"|669.29034423828125,0.01186771504581,1,"b6-H2O1+"|699.23114013671875,0.020817343145609,1,"b4+U-H3PO4"|730.42572021484375,0.26859325170517,1,"y6"|749.25885009765625,8.758146315813065e-03,1,"PMIT+U-H2O"|782.404296875,0.012716175056994,1,"EPMITLP"|784.31610107421875,7.947030477225781e-03,1,"a5+U-H3PO4"|812.31365966796875,0.012815644964576,1,"b5+U-H3PO4"|825.46112060546875,0.037652637809515,1,"y5+U-H3PO4"|827.4814453125,0.037520926445723,1,"y7"|842.45953369140625,0.042362816631794,1,"y6+U'"|879.48016357421875,0.099386416375637,1,"y7+C3O"|939.5068359375,0.254053741693497,1,"y8-H3N1+"|956.483642578125,0.047358602285385,1,"y6+U-H3PO4"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1071.533935546875,0.012802372686565,1,"[M+H]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4"|1133.5010986328125,0.05346042662859,1,"y7+U-H2O"|1151.51953125,0.053188119083643,1,"y7+U"|1183.5704345703125,0.054004456847906,1,"[M+H]+ U'" 37.864 698.2974 DECOY_Cse1 PMVNDNILR U 2 39.625930786132813 2 0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 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112.050773620605469,0.042819745838642,1,"MI:C'"|136.061843872070313,0.196844235062599,1,"MI:A'"|152.056671142578125,0.023113740608096,1,"MI:G'"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1"|182.092300415039063,0.052632980048656,1,"iP+U'"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2"|253.100723266601563,9.467311203479767e-03,1,"PM-CO+C3O"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2"|281.09564208984375,9.001040831208229e-03,1,"PM+C3O"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|313.13702392578125,0.016673086211085,1,"PM-CO+U'"|341.126983642578125,0.080299213528633,1,"PM+U'"|348.068084716796875,9.060680866241455e-03,1,"MI:A"|376.089996337890625,0.029012143611908,1,"iP+U-H2O"|385.25506591796875,0.261529922485352,1,"y3"|394.095611572265625,0.040202785283327,1,"iP+U"|426.217559814453125,7.179270498454571e-03,1,"PMI-CO+U'"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O"|454.151214599609375,0.077750355005264,1,"b3+U'"|454.217010498046875,7.962716743350029e-03,1,"PMI+U'"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4"|525.14324951171875,0.028857138007879,1,"PM-CO+U"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"PM+U-H2O"|537.2529296875,9.177219122648239e-03,1,"PMIT+U'-H2O"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|553.13372802734375,0.032937977463007,1,"PM+U"|553.27215576171875,0.012286836281419,1,"MITL+U'-H2O"|555.264404296875,9.468427859246731e-03,1,"PMIT+U'"|567.26251220703125,0.116328254342079,2,"y7+U-H2O"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U"|585.19580078125,8.00114031881094e-03,1,"b4+U'"|599.387451171875,0.483213186264038,1,"y5"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]++ 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U'"112.050773620605469,0.042819745838642,1,"MI:C'"|136.061843872070313,0.196844235062599,1,"MI:A'"|152.056671142578125,0.023113740608096,1,"MI:G'"|153.1024169921875,0.012729996815324,1,"a2-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1"|182.092300415039063,0.052632980048656,1,"a1+U'"|227.065277099609375,0.01328039355576,1,"MI:U-H3PO4"|245.076187133789063,0.142766728997231,1,"MI:U-HPO3"|253.100723266601563,9.467311203479767e-03,1,"a2+C3O"|281.09564208984375,9.001040831208229e-03,1,"b2+C3O"|288.20294189453125,8.992226794362068e-03,1,"y2"|296.12347412109375,0.02242861315608,1,"a1+U-H3PO4"|313.13702392578125,0.016673086211085,1,"a2+U'"|341.126983642578125,0.080299213528633,1,"b2+U'"|348.068084716796875,9.060680866241455e-03,1,"MI:A"|376.089996337890625,0.029012143611908,1,"a1+U-H2O"|394.095611572265625,0.040202785283327,1,"a1+U"|427.164215087890625,0.022860564291477,1,"a2+U-H3PO4"|525.14324951171875,0.028857138007879,1,"a2+U"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"b2+U-H2O"|553.13372802734375,0.032937977463007,1,"b2+U"|553.27215576171875,0.012286836281419,1,"NDNIL-H3N1+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]++ U-H3PO4"|649.3082275390625,0.248698011040688,2,"[M+2H]++ U-H3PO4"|669.29034423828125,0.01186771504581,1,"MVNDNI-H2O1+"|825.46112060546875,0.037652637809515,1,"y7-H2O1+"|956.483642578125,0.047358602285385,1,"y8-H2O1+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4"|1183.5704345703125,0.054004456847906,1,"[M+H]+ U'"112.050773620605469,0.042819745838642,1,"MI:C'"|129.102310180664063,0.027272067964077,1,"iK(C6H13N2O)"|136.061843872070313,0.196844235062599,1,"MI:A'"|136.074722290039063,0.020733870565891,1,"iK(C5H10N1)C3O"|152.056671142578125,0.023113740608096,1,"MI:G'"|153.1024169921875,0.012729996815324,1,"iK+C3O"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1"|227.065277099609375,0.01328039355576,1,"MI:U-H3PO4"|245.076187133789063,0.142766728997231,1,"MI:U-HPO3"|348.068084716796875,9.060680866241455e-03,1,"MI:A"|385.25506591796875,0.261529922485352,1,"a4"|1055.4859619140625,9.314105845987797e-03,1,"[M+H-NH3]+ U-H3PO4"|1072.548095703125,7.815494202077389e-03,1,"[M+H]+ U-H3PO4" 39.118 623.2540 Cse2 MLTWWGK U 2 48.237815856933594 1 1.08866548538208 0,0.95,0,108.87,16.34,0,7.64 MLTwWGK 920.4578 324.0359 1244.4937 3.611835241317749 2.463027238845825 1 1 1 0 0.372912466526032 0.0 0.215587794780731 2 315.0 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 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diff --git a/src/tests/topp/OpenNuXL_4_output.idXML b/src/tests/topp/OpenNuXL_4_output.idXML index d7c61a6542a..f79f5dc767c 100644 --- a/src/tests/topp/OpenNuXL_4_output.idXML +++ b/src/tests/topp/OpenNuXL_4_output.idXML @@ -6,7 +6,7 @@ - + @@ -61,7 +61,7 @@ - + @@ -69,7 +69,7 @@ - + @@ -141,7 +141,7 @@ - + @@ -149,7 +149,7 @@ - + @@ -221,7 +221,7 @@ - + @@ -229,7 +229,7 @@ - + @@ -301,7 +301,7 @@ - + @@ -309,7 +309,7 @@ - + @@ -359,78 +359,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -453,7 +381,7 @@ - + @@ -461,7 +389,7 @@ - + @@ -533,7 +461,7 @@ - + @@ -541,7 +469,7 @@ - + @@ -609,7 +537,7 @@ - + @@ -617,7 +545,7 @@ - + @@ -685,7 +613,7 @@ - + @@ -693,7 +621,7 @@ - + @@ -761,7 +689,7 @@ - + @@ -769,7 +697,7 @@ - + @@ -837,7 +765,7 @@ - + @@ -845,7 +773,7 @@ - + @@ -895,48 +823,48 @@ - - + + - + - + - - - - + + + + - - - - - - + + + + + + - - + + - - + + - - + + - + - - - - + + 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a/src/tests/topp/OpenNuXL_4_output2.tsv b/src/tests/topp/OpenNuXL_4_output2.tsv index 4229a0d701e..24a2738bc65 100644 --- a/src/tests/topp/OpenNuXL_4_output2.tsv +++ b/src/tests/topp/OpenNuXL_4_output2.tsv @@ -3,14 +3,13 @@ 18.306 590.7661 Cas6e LDSKGNIK U-H2O1 2 25.741664886474609 1 2.196093797683716 0,0,0,219.61,0,0,0,8.00 LDSkGNIK 873.4920 306.0253 1179.5173 2.428377628326416 4.320775508880615 1 1 1 0 0.130456954240799 0.0 0.175812318921089 1 315.0 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O" 25.116 508.1855 Cas5 YTPYLGR AU 3 40.562583923339844 1 0.734427034854889 0,0.24,0,73.44,0,0,0 YTPyLGR 868.4443 653.0884 1521.5327 3.710045576095581 2.351816177368164 1 1 1 0 0.190965637564659 0.0 0.210292190313339 1 315.0 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 136.0615234375,1.0,1,"MI:A'"|136.07513427734375,0.229426234960556,1,"a1"|152.05633544921875,4.265095572918654e-03,1,"MI:G'"|158.092025756835938,9.572696872055531e-03,1,"y1-H3N1+"|164.070541381835938,3.483457025140524e-03,1,"b1"|175.119049072265625,0.031937755644321,1,"y1"|215.114288330078125,7.323490455746651e-03,1,"y2-H3N1+"|219.112014770507813,7.127284072339535e-03,1,"a2-H2O1+"|232.140228271484375,0.069322824478149,1,"y2"|237.123199462890625,0.195591405034065,1,"a2"|247.107315063476563,2.211090410128236e-03,1,"b2-H2O1+"|265.118011474609375,0.063581943511963,1,"b2"|285.1221923828125,7.153767161071301e-03,1,"PY-CO+C3O"|313.116943359375,3.152150195091963e-03,1,"PY+C3O"|327.1427001953125,1.970470184460282e-03,1,"PY-CO+U'-H2O"|328.198333740234375,2.614108612760902e-03,1,"y3-H3N1+"|329.17095947265625,0.072819426655769,2,"y5+C3O"|345.15252685546875,2.646437846124172e-03,1,"PY-CO+U'"|345.224029541015625,0.10897596180439,1,"y3"|348.06982421875,0.043133333325386,1,"MI:A"|359.1365966796875,2.3593760561198e-03,1,"b2+U'-H2O"|359.186859130859375,0.098186790943146,2,"y5+U'"|373.151611328125,2.350400667637587e-03,1,"PY+U'"|389.189697265625,2.83268908970058e-03,1,"YL+U'"|456.184844970703125,0.019872423261404,2,"y5+U-H2O"|465.191619873046875,0.025686334818602,2,"y5+U"|560.28369140625,0.03523913398385,1,"y4+C3O"|620.31134033203125,0.013985485769808,1,"b5-H2O1+"|657.33489990234375,0.3373843729496,1,"y5+C3O"|717.36590576171875,0.067729890346527,1,"y5+U'"|734.35107421875,3.099862718954682e-03,1,"y4+U-H3PO4"|758.38824462890625,0.013845652341843,1,"y6+C3O"|831.39337158203125,9.685350582003594e-03,1,"y5+U-H3PO4"|849.408447265625,4.016013350337744e-03,1,"y5+U-HPO3"|903.43212890625,2.896269550547004e-03,1,"[M+H-H2O]+ C3O"|911.36871337890625,0.012803317978978,1,"y5+U-H2O"|921.44696044921875,0.019729314371943,1,"[M+H]+ C3O"|929.37530517578125,0.034058455377817,1,"y5+U" 26.237 678.2844 Cas5 DYHTVLGAR U 2 67.563796997070313 1 0.892229020595551 0,89.22,0,0,23.58,0,0,0,0 DyHTVLGAR 1030.5196 324.0359 1354.5555 12.389053344726563 8.871867179870606 1 1 1 0 0.218422010540962 0.0 0.070792749524117 3 315.0 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 110.071525573730469,0.124598376452923,1,"iH+"|112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|204.134170532226563,0.047920491546392,1,"y2-C1H2N2+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|229.127822875976563,6.706117186695337e-03,1,"y2-H3N1+"|239.113800048828125,7.95002281665802e-03,1,"HT"|246.155319213867188,0.029895069077611,1,"y2"|286.150421142578125,0.037254326045513,1,"y3-H3N1+"|303.177154541015625,0.322829812765121,1,"y3"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|368.21673583984375,0.152305349707603,2,"y7-H2O1++"|377.221343994140625,0.194865599274635,2,"y7"|399.233306884765625,0.032629072666168,1,"y4-H3N1+"|415.200531005859375,0.011067586950958,1,"y3+U'"|416.16107177734375,9.909789077937603e-03,1,"b3"|416.2611083984375,0.390764862298965,1,"y4"|423.222259521484375,0.047973766922951,1,"TVLG+C3O"|477.163330078125,0.041644386947155,1,"a2+U-H3PO4"|499.19189453125,8.276323787868023e-03,1,"b4-H2O1+"|505.15753173828125,0.058943208307028,1,"b2+U-H3PO4"|510.177032470703125,9.497386403381825e-03,1,"b3+U'-H2O"|515.33038330078125,0.247247070074081,1,"y5"|517.205078125,0.010058866813779,1,"b4"|527.185791015625,0.053621523082256,1,"YH+U-H3PO4"|571.7821044921875,0.309090524911881,2,"y8+U-H3PO4"|598.37109375,0.028361488133669,1,"y6-H2O1+"|614.22186279296875,0.011790351010859,1,"a3+U-H3PO4"|616.3775634765625,0.524602711200714,1,"y6"|620.29071044921875,0.307169079780579,2,"[M+2H-H2O]++ U-H3PO4"|629.2969970703125,1.0,2,"[M+2H-H2O]++ U-HPO3"|642.2138671875,0.065313711762428,1,"b3+U-H3PO4"|660.23907470703125,0.030145548284054,1,"b3+U-HPO3"|669.27935791015625,0.066578842699528,2,"[M+2H-H2O]++ U"|722.1842041015625,0.012603042647243,1,"b3+U-H2O"|735.421142578125,0.030300982296467,1,"y7-H2O1+"|740.19207763671875,0.010872688144445,1,"b3+U"|743.26336669921875,0.047368142753839,1,"b4+U-H3PO4"|753.4393310546875,0.262213468551636,1,"y7"|814.327880859375,0.01301802136004,1,"HTVLG+U-H2O"|842.3365478515625,0.057222794741392,1,"b5+U-H3PO4"|898.3970947265625,0.025343561545014,1,"b7+U'"|909.42108154296875,0.010454332455993,1,"b8+C3O"|916.491455078125,0.011721312068403,1,"y8"|927.43896484375,0.037982285022736,1,"a6+U-H3PO4"|955.418212890625,0.050513833761215,1,"b6+U-H3PO4"|1025.4136962890625,0.029244165867567,1,"a6+U"|1031.5264892578125,0.180062636733055,1,"[M+H]+"|1083.4879150390625,0.025055043399334,1,"b8+U-H3PO4"|1143.546875,0.033915352076292,1,"[M+H]+ U'" -26.237 678.2844 DECOY_Cse1 QLNYIQDR U-H2O1 2 14.15965747833252 2 0.059144008904696 0,0,0,5.91,0,0,0,0 QLNyIQDR 1048.5302 306.0253 1354.5555 12.389053344726563 8.871867179870606 1 1 1 0 0.218422010540962 0.0 0.070792749524117 3 315.0 0 0.156072795391083 0.037278719246387 0.018650691956282 0.0 0.014469237066805 3 315.0 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 110.071525573730469,0.124598376452923,1,"iH+"|112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|204.134170532226563,0.047920491546392,1,"y2-C1H2N2+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|229.127822875976563,6.706117186695337e-03,1,"y2-H3N1+"|239.113800048828125,7.95002281665802e-03,1,"HT"|246.155319213867188,0.029895069077611,1,"y2"|286.150421142578125,0.037254326045513,1,"y3-H3N1+"|303.177154541015625,0.322829812765121,1,"y3"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|368.21673583984375,0.152305349707603,2,"y7-H2O1++"|377.221343994140625,0.194865599274635,2,"y7"|399.233306884765625,0.032629072666168,1,"y4-H3N1+"|415.200531005859375,0.011067586950958,1,"y3+U'"|416.16107177734375,9.909789077937603e-03,1,"b3"|416.2611083984375,0.390764862298965,1,"y4"|423.222259521484375,0.047973766922951,1,"TVLG+C3O"|477.163330078125,0.041644386947155,1,"a2+U-H3PO4"|499.19189453125,8.276323787868023e-03,1,"b4-H2O1+"|505.15753173828125,0.058943208307028,1,"b2+U-H3PO4"|510.177032470703125,9.497386403381825e-03,1,"b3+U'-H2O"|515.33038330078125,0.247247070074081,1,"y5"|517.205078125,0.010058866813779,1,"b4"|527.185791015625,0.053621523082256,1,"YH+U-H3PO4"|571.7821044921875,0.309090524911881,2,"y8+U-H3PO4"|598.37109375,0.028361488133669,1,"y6-H2O1+"|614.22186279296875,0.011790351010859,1,"a3+U-H3PO4"|616.3775634765625,0.524602711200714,1,"y6"|620.29071044921875,0.307169079780579,2,"[M+2H-H2O]++ U-H3PO4"|629.2969970703125,1.0,2,"[M+2H-H2O]++ U-HPO3"|642.2138671875,0.065313711762428,1,"b3+U-H3PO4"|660.23907470703125,0.030145548284054,1,"b3+U-HPO3"|669.27935791015625,0.066578842699528,2,"[M+2H-H2O]++ U"|722.1842041015625,0.012603042647243,1,"b3+U-H2O"|735.421142578125,0.030300982296467,1,"y7-H2O1+"|740.19207763671875,0.010872688144445,1,"b3+U"|743.26336669921875,0.047368142753839,1,"b4+U-H3PO4"|753.4393310546875,0.262213468551636,1,"y7"|814.327880859375,0.01301802136004,1,"HTVLG+U-H2O"|842.3365478515625,0.057222794741392,1,"b5+U-H3PO4"|898.3970947265625,0.025343561545014,1,"b7+U'"|909.42108154296875,0.010454332455993,1,"b8+C3O"|916.491455078125,0.011721312068403,1,"y8"|927.43896484375,0.037982285022736,1,"a6+U-H3PO4"|955.418212890625,0.050513833761215,1,"b6+U-H3PO4"|1025.4136962890625,0.029244165867567,1,"a6+U"|1031.5264892578125,0.180062636733055,1,"[M+H]+"|1083.4879150390625,0.025055043399334,1,"b8+U-H3PO4"|1143.546875,0.033915352076292,1,"[M+H]+ U'"112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|197.128097534179688,0.027758901938796,1,"a2-H3N1+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|415.200531005859375,0.011067586950958,1,"LNY-CO+C3O"|544.24188232421875,0.022189674898982,1,"YIQD-CO+C3O"|555.177978515625,0.011142131872475,1,"YI-CO+U-H2O"|598.28643798828125,0.048303849995136,1,"LNYI+U'-H2O"|629.2969970703125,1.0,2,"[M+2H-H2O]++ U-H3PO4"|669.27935791015625,0.066578842699528,2,"[M+2H-H2O]++ U-H2O"|927.43896484375,0.037982285022736,1,"b7+C3O"|1025.4136962890625,0.029244165867567,1,"LNYIQD-CO+U-H2O"|1031.5264892578125,0.180062636733055,1,"[M+H-H2O]+"|1143.546875,0.033915352076292,1,"[M+H]+ U'-H2O" 26.413 791.8590 Cse2 KSEQTTGISLGR U-H2O1 2 59.922630310058594 1 0.718522191047669 71.85,28.95,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 19.087356567382813 10.870758056640625 1 1 1 0 0.221869960427284 0.0 0.115903504192829 2 315.0 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 112.050689697265625,9.990843944251537e-03,1,"MI:C'"|129.102371215820313,0.013408292084932,1,"b1"|136.061798095703125,0.902763903141022,1,"MI:A'"|136.074905395507813,0.051667388528585,1,"iK(C5H10N1)C3O"|152.056564331054688,3.377486718818545e-03,1,"MI:G'"|158.092697143554688,0.024075241759419,1,"y1-H3N1+"|175.118927001953125,0.081427209079266,1,"y1"|178.097412109375,0.341100573539734,1,"iK(C5H10N1)U'-H2O"|195.123382568359375,0.017177894711494,1,"a1+U'-H2O"|215.113723754882813,0.014229998923838,1,"y2-H3N1+"|227.066909790039063,0.016493165865541,1,"MI:U-H3PO4"|232.140274047851563,0.180095225572586,1,"y2"|241.1295166015625,0.01908091455698,1,"b1+U'"|258.143798828125,3.849325468763709e-03,1,"GIS"|282.156463623046875,0.019274268299341,1,"a2+U'-H2O"|310.150787353515625,0.118582129478455,1,"b2+U'-H2O"|327.212188720703125,3.42642655596137e-03,1,"y3-H2O1+"|328.199676513671875,4.501644056290388e-03,1,"y3-H3N1+"|345.223907470703125,0.247861370444298,1,"y3"|348.0692138671875,7.973242551088333e-03,1,"MI:A"|428.180908203125,8.386147208511829e-03,1,"SEQT-H2O1+"|432.25604248046875,0.183289110660553,1,"y4"|439.19366455078125,0.044542569667101,1,"b3+U'-H2O"|490.216064453125,0.052840437740088,2,"QTTGISL-CO+U-H2O"|517.22088623046875,3.666676813736558e-03,1,"EQTTG"|529.219970703125,9.659912437200546e-03,1,"SEQTT-H2O1+"|545.3385009765625,0.023281643167138,1,"TTGISL-CO"|567.25286865234375,0.052726376801729,1,"b4+U'-H2O"|602.3612060546875,0.080439247190952,1,"TTGISLG-CO"|676.849365234375,0.461511492729187,2,"[M+2H-H2O]++ 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112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" 33.237 510.2805 DECOY_Cas7 LKLLVK U-H2O1 2 30.675045013427734 2 1.106894612312317 0,110.69,77.01,0,0,27.74 LkLLVK 712.5211 306.0253 1018.5464 2.676236867904663 4.84662389755249 1 1 1 0 0.182740524411201 0.0 0.375015050172806 2 315.0 0 1.17647397518158 4.721068859100342 0.079879306256771 0.0 0.211029142141342 2 315.0 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"LL-CO"|227.175506591796875,0.098765894770622,1,"LL"|242.18536376953125,0.01018890645355,1,"b2"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|336.201568603515625,0.059393648058176,1,"b2+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"b4+C3O"|548.35498046875,0.371608823537827,1,"KLLV+U'-H2O"|562.3695068359375,0.036407515406609,1,"b4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" 33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 31.678943634033203 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 0.0 0.059569962322712 2 315.0 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" @@ -24,5 +23,4 @@ 37.864 698.2974 DECOY_Cse1 PMVNDNILR U 2 39.625930786132813 2 0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 112.050773620605469,0.042819745838642,1,"MI:C'"|136.061843872070313,0.196844235062599,1,"MI:A'"|152.056671142578125,0.023113740608096,1,"MI:G'"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1"|182.092300415039063,0.052632980048656,1,"iP+U'"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2"|253.100723266601563,9.467311203479767e-03,1,"PM-CO+C3O"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2"|281.09564208984375,9.001040831208229e-03,1,"PM+C3O"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|313.13702392578125,0.016673086211085,1,"PM-CO+U'"|341.126983642578125,0.080299213528633,1,"PM+U'"|348.068084716796875,9.060680866241455e-03,1,"MI:A"|376.089996337890625,0.029012143611908,1,"iP+U-H2O"|385.25506591796875,0.261529922485352,1,"y3"|394.095611572265625,0.040202785283327,1,"iP+U"|426.217559814453125,7.179270498454571e-03,1,"PMI-CO+U'"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O"|454.151214599609375,0.077750355005264,1,"b3+U'"|454.217010498046875,7.962716743350029e-03,1,"PMI+U'"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4"|525.14324951171875,0.028857138007879,1,"PM-CO+U"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"PM+U-H2O"|537.2529296875,9.177219122648239e-03,1,"PMIT+U'-H2O"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|553.13372802734375,0.032937977463007,1,"PM+U"|553.27215576171875,0.012286836281419,1,"MITL+U'-H2O"|555.264404296875,9.468427859246731e-03,1,"PMIT+U'"|567.26251220703125,0.116328254342079,2,"y7+U-H2O"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U"|585.19580078125,8.00114031881094e-03,1,"b4+U'"|599.387451171875,0.483213186264038,1,"y5"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]++ U-H3PO4"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O"|649.3082275390625,0.248698011040688,2,"[M+2H]++ U-H3PO4"|669.29034423828125,0.01186771504581,1,"b6-H2O1+"|699.23114013671875,0.020817343145609,1,"b4+U-H3PO4"|730.42572021484375,0.26859325170517,1,"y6"|749.25885009765625,8.758146315813065e-03,1,"PMIT+U-H2O"|782.404296875,0.012716175056994,1,"EPMITLP"|784.31610107421875,7.947030477225781e-03,1,"a5+U-H3PO4"|812.31365966796875,0.012815644964576,1,"b5+U-H3PO4"|825.46112060546875,0.037652637809515,1,"y5+U-H3PO4"|827.4814453125,0.037520926445723,1,"y7"|842.45953369140625,0.042362816631794,1,"y6+U'"|879.48016357421875,0.099386416375637,1,"y7+C3O"|939.5068359375,0.254053741693497,1,"y8-H3N1+"|956.483642578125,0.047358602285385,1,"y6+U-H3PO4"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1071.533935546875,0.012802372686565,1,"[M+H]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4"|1133.5010986328125,0.05346042662859,1,"y7+U-H2O"|1151.51953125,0.053188119083643,1,"y7+U"|1183.5704345703125,0.054004456847906,1,"[M+H]+ U'"112.050773620605469,0.042819745838642,1,"MI:C'"|136.061843872070313,0.196844235062599,1,"MI:A'"|152.056671142578125,0.023113740608096,1,"MI:G'"|153.1024169921875,0.012729996815324,1,"a2-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1"|182.092300415039063,0.052632980048656,1,"a1+U'"|227.065277099609375,0.01328039355576,1,"MI:U-H3PO4"|245.076187133789063,0.142766728997231,1,"MI:U-HPO3"|253.100723266601563,9.467311203479767e-03,1,"a2+C3O"|281.09564208984375,9.001040831208229e-03,1,"b2+C3O"|288.20294189453125,8.992226794362068e-03,1,"y2"|296.12347412109375,0.02242861315608,1,"a1+U-H3PO4"|313.13702392578125,0.016673086211085,1,"a2+U'"|341.126983642578125,0.080299213528633,1,"b2+U'"|348.068084716796875,9.060680866241455e-03,1,"MI:A"|376.089996337890625,0.029012143611908,1,"a1+U-H2O"|394.095611572265625,0.040202785283327,1,"a1+U"|427.164215087890625,0.022860564291477,1,"a2+U-H3PO4"|525.14324951171875,0.028857138007879,1,"a2+U"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"b2+U-H2O"|553.13372802734375,0.032937977463007,1,"b2+U"|553.27215576171875,0.012286836281419,1,"NDNIL-H3N1+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]++ U-H3PO4"|649.3082275390625,0.248698011040688,2,"[M+2H]++ U-H3PO4"|669.29034423828125,0.01186771504581,1,"MVNDNI-H2O1+"|825.46112060546875,0.037652637809515,1,"y7-H2O1+"|956.483642578125,0.047358602285385,1,"y8-H2O1+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4"|1183.5704345703125,0.054004456847906,1,"[M+H]+ U'" 39.118 623.2540 Cse2 MLTWWGK U 2 48.237815856933594 1 1.08866548538208 0,0.95,0,108.87,16.34,0,7.64 MLTwWGK 920.4578 324.0359 1244.4937 3.611835241317749 2.463027238845825 1 1 1 0 0.372912466526032 0.0 0.215587794780731 2 315.0 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 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U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" 39.853 861.3889 Cas5 LAGPMQAWGQPTFEGTRPTGR U 3 37.401420593261719 1 2.457196474075317 0,0,0,0,0,0,0,0,244.47,0,0,0,0,0,0,0,0,0,245.72,0,0 LAGPMQAWGQPTFEGTRPtGR 2257.1062 324.0359 2581.1421 9.457996368408203 11.046560287475586 1 1 1 0 0.13300721347332 0.0 0.168000027537346 2 315.0 0 14.94 3.38 3.08 0.00 1.95 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 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diff --git a/src/tests/topp/OpenNuXL_5_output.idXML b/src/tests/topp/OpenNuXL_5_output.idXML index abad85a2ddd..c46c4219bf7 100644 --- a/src/tests/topp/OpenNuXL_5_output.idXML +++ b/src/tests/topp/OpenNuXL_5_output.idXML @@ -6,7 +6,7 @@ - + @@ -49,7 +49,7 @@ - + @@ -57,7 +57,7 @@ - + @@ -78,7 +78,7 @@ - + @@ -129,7 +129,7 @@ - + @@ -137,7 +137,7 @@ - + @@ -158,7 +158,7 @@ - + @@ -209,7 +209,7 @@ - + @@ -217,7 +217,7 @@ - + @@ -238,7 +238,7 @@ - + @@ -289,7 +289,7 @@ - + @@ -297,7 +297,7 @@ - + @@ -318,7 +318,7 @@ - + @@ -369,7 +369,7 @@ - + @@ -377,7 +377,7 @@ - + @@ -398,7 +398,7 @@ - + @@ -449,7 +449,7 @@ - + @@ -457,7 +457,7 @@ - + @@ -478,7 +478,7 @@ - + @@ -529,7 +529,7 @@ - + @@ -537,7 +537,7 @@ - + @@ -558,7 +558,7 @@ - + @@ -609,7 +609,7 @@ - + @@ -617,7 +617,7 @@ - + @@ -638,7 +638,7 @@ - + @@ -689,7 +689,7 @@ - + @@ -697,7 +697,7 @@ - + @@ -718,7 +718,7 @@ - + @@ -769,7 +769,7 @@ - + @@ -777,7 +777,7 @@ - + @@ -798,7 +798,7 @@ - + @@ -849,7 +849,7 @@ - + @@ -857,7 +857,7 @@ - + @@ -878,7 +878,7 @@ - + @@ -929,7 +929,7 @@ - + @@ -937,7 +937,7 @@ - + @@ -958,7 +958,7 @@ - + @@ -1009,7 +1009,7 @@ - + @@ -1017,7 +1017,7 @@ - + @@ -1038,7 +1038,7 @@ - + @@ -1089,7 +1089,7 @@ - + @@ -1097,7 +1097,7 @@ - + @@ -1118,7 +1118,7 @@ - + @@ -1169,7 +1169,7 @@ - + @@ -1177,7 +1177,7 @@ - + @@ -1198,7 +1198,7 @@ - + @@ -1249,7 +1249,7 @@ - + @@ -1257,7 +1257,7 @@ - + @@ -1278,7 +1278,7 @@ - + @@ -1329,7 +1329,7 @@ - + @@ -1337,7 +1337,7 @@ - + @@ -1358,7 +1358,7 @@ - + @@ -1409,7 +1409,7 @@ - + @@ -1417,7 +1417,7 @@ - + @@ -1438,7 +1438,7 @@ - + @@ -1489,7 +1489,7 @@ - + @@ -1497,7 +1497,7 @@ - + @@ -1518,7 +1518,7 @@ - + @@ -1569,7 +1569,7 @@ - + @@ -1577,7 +1577,7 @@ - + @@ -1598,7 +1598,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_6_output.idXML b/src/tests/topp/OpenNuXL_6_output.idXML index 1069df2befa..cb76bda8321 100644 --- a/src/tests/topp/OpenNuXL_6_output.idXML +++ b/src/tests/topp/OpenNuXL_6_output.idXML @@ -6,7 +6,7 @@ - + @@ -53,7 +53,7 @@ - + @@ -61,7 +61,7 @@ - + @@ -82,7 +82,7 @@ - + @@ -129,7 +129,7 @@ - + @@ -137,7 +137,7 @@ - + @@ -158,7 +158,7 @@ - + @@ -205,7 +205,7 @@ - + @@ -213,7 +213,7 @@ - + @@ -234,7 +234,7 @@ - + @@ -277,7 +277,7 @@ - + @@ -285,7 +285,7 @@ - + @@ -306,7 +306,7 @@ - + @@ -357,7 +357,7 @@ - + @@ -365,7 +365,7 @@ - + @@ -386,7 +386,7 @@ - + @@ -433,7 +433,7 @@ - + @@ -441,7 +441,7 @@ - + @@ -462,7 +462,7 @@ - + @@ -509,7 +509,7 @@ - + @@ -517,7 +517,7 @@ - + @@ -538,7 +538,7 @@ - + @@ -585,7 +585,7 @@ - + @@ -593,7 +593,7 @@ - + @@ -614,7 +614,7 @@ - + @@ -661,7 +661,7 @@ - + @@ -669,7 +669,7 @@ - + @@ -690,7 +690,7 @@ - + @@ -737,7 +737,7 @@ - + @@ -745,7 +745,7 @@ - + @@ -766,7 +766,7 @@ - + @@ -813,7 +813,7 @@ - + @@ -821,7 +821,7 @@ - + @@ -842,7 +842,7 @@ - + @@ -889,7 +889,7 @@ - + @@ -897,7 +897,7 @@ - + @@ -918,7 +918,7 @@ - + @@ -965,7 +965,7 @@ - + @@ -973,7 +973,7 @@ - + @@ -994,7 +994,7 @@ - + @@ -1041,7 +1041,7 @@ - + @@ -1049,7 +1049,7 @@ - + @@ -1070,7 +1070,7 @@ - + @@ -1117,7 +1117,7 @@ - + @@ -1125,7 +1125,7 @@ - + @@ -1146,7 +1146,7 @@ - + @@ -1193,7 +1193,7 @@ - + @@ -1201,7 +1201,7 @@ - + @@ -1222,7 +1222,7 @@ - + @@ -1269,7 +1269,7 @@ - + @@ -1277,7 +1277,7 @@ - + @@ -1298,7 +1298,7 @@ - + @@ -1345,7 +1345,7 @@ - + @@ -1353,7 +1353,7 @@ - + @@ -1374,7 +1374,7 @@ - + @@ -1421,7 +1421,7 @@ - + @@ -1429,7 +1429,7 @@ - + @@ -1450,7 +1450,7 @@ - + @@ -1497,7 +1497,7 @@ - + @@ -1505,7 +1505,7 @@ - + @@ -1526,7 +1526,7 @@ - + @@ -1573,7 +1573,7 @@ - + @@ -1581,7 +1581,7 @@ - + @@ -1602,7 +1602,7 @@ - + @@ -1649,7 +1649,7 @@ - + @@ -1657,7 +1657,7 @@ - + @@ -1678,7 +1678,7 @@ - + @@ -1725,7 +1725,7 @@ - + @@ -1733,7 +1733,7 @@ - + @@ -1754,7 +1754,7 @@ - + @@ -1805,7 +1805,7 @@ - + @@ -1813,7 +1813,7 @@ - + @@ -1834,7 +1834,7 @@ - + @@ -1881,7 +1881,7 @@ - + @@ -1889,7 +1889,7 @@ - + @@ -1910,7 +1910,7 @@ - + @@ -1957,7 +1957,7 @@ - + @@ -1965,7 +1965,7 @@ - + @@ -1986,7 +1986,7 @@ - + @@ -2029,7 +2029,7 @@ - + @@ -2037,7 +2037,7 @@ - + @@ -2058,7 +2058,7 @@ - + @@ -2105,7 +2105,7 @@ - + @@ -2113,7 +2113,7 @@ - + @@ -2134,7 +2134,7 @@ - + @@ -2181,7 +2181,7 @@ - + @@ -2189,7 +2189,7 @@ - + @@ -2210,7 +2210,7 @@ - + @@ -2257,7 +2257,7 @@ - + @@ -2265,7 +2265,7 @@ - + @@ -2286,7 +2286,7 @@ - + @@ -2333,7 +2333,7 @@ - + @@ -2341,7 +2341,7 @@ - + @@ -2362,7 +2362,7 @@ - + @@ -2409,7 +2409,7 @@ - + @@ -2417,7 +2417,7 @@ - + @@ -2438,7 +2438,7 @@ - + @@ -2485,7 +2485,7 @@ - + @@ -2493,7 +2493,7 @@ - + @@ -2514,7 +2514,7 @@ - + @@ -2561,7 +2561,7 @@ - + @@ -2569,7 +2569,7 @@ - + @@ -2590,7 +2590,7 @@ - + @@ -2637,7 +2637,7 @@ - + @@ -2645,7 +2645,7 @@ - + @@ -2666,7 +2666,7 @@ - + @@ -2713,7 +2713,7 @@ - + @@ -2721,7 +2721,7 @@ - + @@ -2742,7 +2742,7 @@ - + @@ -2789,7 +2789,7 @@ - + @@ -2797,7 +2797,7 @@ - + @@ -2818,7 +2818,7 @@ - + @@ -2865,7 +2865,7 @@ - + @@ -2873,7 +2873,7 @@ - + @@ -2894,7 +2894,7 @@ - + @@ -2945,7 +2945,7 @@ - + @@ -2953,7 +2953,7 @@ - + @@ -2974,7 +2974,7 @@ - + @@ -3021,7 +3021,7 @@ - + @@ -3029,7 +3029,7 @@ - + @@ -3050,7 +3050,7 @@ - + @@ -3097,7 +3097,7 @@ - + @@ -3105,7 +3105,7 @@ - + @@ -3126,7 +3126,7 @@ - + @@ -3173,7 +3173,7 @@ - + @@ -3181,7 +3181,7 @@ - + @@ -3202,7 +3202,7 @@ - + @@ -3253,7 +3253,7 @@ - + @@ -3261,7 +3261,7 @@ - + @@ -3282,7 +3282,7 @@ - + @@ -3329,7 +3329,7 @@ - + @@ -3337,7 +3337,7 @@ - + @@ -3358,7 +3358,7 @@ - + @@ -3405,7 +3405,7 @@ - + @@ -3413,7 +3413,7 @@ - + @@ -3434,7 +3434,7 @@ - + @@ -3481,7 +3481,7 @@ - + @@ -3489,7 +3489,7 @@ - + @@ -3510,7 +3510,7 @@ - + @@ -3557,7 +3557,7 @@ - + @@ -3565,7 +3565,7 @@ - + @@ -3586,7 +3586,7 @@ - + @@ -3633,7 +3633,7 @@ - + @@ -3641,7 +3641,7 @@ - + @@ -3662,7 +3662,7 @@ - + @@ -3709,7 +3709,7 @@ - + @@ -3717,7 +3717,7 @@ - + @@ -3738,7 +3738,7 @@ - + @@ -3785,7 +3785,7 @@ - + @@ -3793,7 +3793,7 @@ - + @@ -3814,7 +3814,7 @@ - + @@ -3865,7 +3865,7 @@ - + @@ -3873,7 +3873,7 @@ - + @@ -3894,7 +3894,7 @@ - + @@ -3941,7 +3941,7 @@ - + @@ -3949,7 +3949,7 @@ - + @@ -3970,7 +3970,7 @@ - + @@ -4017,7 +4017,7 @@ - + @@ -4025,7 +4025,7 @@ - + @@ -4046,7 +4046,7 @@ - + @@ -4093,7 +4093,7 @@ - + @@ -4101,7 +4101,7 @@ - + @@ -4122,7 +4122,7 @@ - + @@ -4173,7 +4173,7 @@ - + @@ -4181,7 +4181,7 @@ - + @@ -4202,7 +4202,7 @@ - + @@ -4249,7 +4249,7 @@ - + @@ -4257,7 +4257,7 @@ - + @@ -4278,7 +4278,7 @@ - + @@ -4325,7 +4325,7 @@ - + @@ -4333,7 +4333,7 @@ - + @@ -4354,7 +4354,7 @@ - + @@ -4401,7 +4401,7 @@ - + @@ -4409,7 +4409,7 @@ - + @@ -4430,7 +4430,7 @@ - + @@ -4477,7 +4477,7 @@ - + @@ -4485,7 +4485,7 @@ - + @@ -4506,7 +4506,7 @@ - + @@ -4553,7 +4553,7 @@ - + @@ -4561,7 +4561,7 @@ - + @@ -4582,7 +4582,7 @@ - + @@ -4629,7 +4629,7 @@ - + @@ -4637,7 +4637,7 @@ - + @@ -4658,7 +4658,7 @@ - + @@ -4705,7 +4705,7 @@ - + @@ -4713,7 +4713,7 @@ - + @@ -4734,7 +4734,7 @@ - + @@ -4781,7 +4781,7 @@ - + @@ -4789,7 +4789,7 @@ - + @@ -4810,7 +4810,7 @@ - + @@ -4857,7 +4857,7 @@ - + @@ -4865,7 +4865,7 @@ - + @@ -4886,7 +4886,7 @@ - + @@ -4933,7 +4933,7 @@ - + @@ -4941,7 +4941,7 @@ - + @@ -4962,7 +4962,7 @@ - + @@ -5009,7 +5009,7 @@ - + @@ -5017,7 +5017,7 @@ - + @@ -5038,7 +5038,7 @@ - + @@ -5085,7 +5085,7 @@ - + @@ -5093,7 +5093,7 @@ - + @@ -5114,7 +5114,7 @@ - + @@ -5161,7 +5161,7 @@ - + @@ -5169,7 +5169,7 @@ - + @@ -5190,7 +5190,7 @@ - + @@ -5237,7 +5237,7 @@ - + @@ -5245,7 +5245,7 @@ - + @@ -5266,7 +5266,7 @@ - + @@ -5309,7 +5309,7 @@ - + @@ -5317,7 +5317,7 @@ - + @@ -5338,7 +5338,7 @@ - + @@ -5389,7 +5389,7 @@ - + @@ -5397,7 +5397,7 @@ - + @@ -5418,7 +5418,7 @@ - + @@ -5465,7 +5465,7 @@ - + @@ -5473,7 +5473,7 @@ - + @@ -5494,7 +5494,7 @@ - + @@ -5541,7 +5541,7 @@ - + @@ -5549,7 +5549,7 @@ - + @@ -5570,7 +5570,7 @@ - + @@ -5617,7 +5617,7 @@ - + @@ -5625,7 +5625,7 @@ - + @@ -5646,7 +5646,7 @@ - + @@ -5697,7 +5697,7 @@ - + @@ -5705,7 +5705,7 @@ - + @@ -5726,7 +5726,7 @@ - + @@ -5773,7 +5773,7 @@ - + @@ -5781,7 +5781,7 @@ - + @@ -5802,7 +5802,7 @@ - + @@ -5849,7 +5849,7 @@ - + @@ -5857,7 +5857,7 @@ - + @@ -5878,7 +5878,7 @@ - + @@ -5925,7 +5925,7 @@ - + @@ -5933,7 +5933,7 @@ - + @@ -5954,7 +5954,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_6_output2.tsv b/src/tests/topp/OpenNuXL_6_output2.tsv index 24aa66b5ff1..893eeb91876 100644 --- a/src/tests/topp/OpenNuXL_6_output2.tsv +++ b/src/tests/topp/OpenNuXL_6_output2.tsv @@ -1,81 +1,81 @@ #RT m/z proteins peptide NA charge score rank best localization score localization scores best localization(s) peptide weight NA weight cross-link weight NuXL:total_loss_score NuXL:partial_loss_score CountSequenceIsTop CountSequenceCharges CountSequenceIsXL CountSequenceIsPeptide NuXL:MIC NuXL:pl_pc_MIC NuXL:pl_MIC nr_candidates -ln(poisson) isotope_error A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H fragment_annotation -17.788 712.7828 Cas7 AEADNLDDKK U-H3O4P1 2 66.026290893554688 1 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 226.0590 1343.5841 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 51.069818780383514 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -39.9835 59428.6 1344.5914 672.7993 448.8686 336.9033 112.050621032714844,0.028104400262237,1,"MI:C'"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O"|501.19091796875,0.035030111670494,1,"b5"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O"|584.267578125,9.894491173326969e-03,1,"LDDK+U'"|586.28167724609375,0.011093857698143,1,"a6"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]++ 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112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O" -18.306 590.7661 Cas6e LDSKGNIK U-H2O1 2 31.744165420532227 2 2.196093797683716 0,0,0,219.61,0,0,0,8.00 LDSkGNIK 873.4920 306.0253 1179.5173 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O" -18.306 590.7661 Cas6e LDSKGNIK none 2 12.331851959228516 3 0.0 0 LDSKGNIK 873.4920 0.0000 873.4920 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.326696595485117 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -153.0128 349541.2 874.4993 437.7533 292.1713 219.3803 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ 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-18.306 590.7661 Cas6e DLYQLHQGLWHLFPNR none 2 8.358111381530762 4 0.0 0 DLYQLHQGLWHLFPNR 2036.0381 0.0000 2036.0381 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 19.072887162391996 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.326696595485117 0 0.948040783405304 0.0 0.042552266269922 0.0 0.0 29253 3.119995027343216 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 428.2603 -420264.2 2037.0453 1019.0263 679.6866 510.0168 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112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" -33.237 510.2805 Cas7 LLKVLK none 2 13.002236366271973 3 0.0 0 LLKVLK 712.5211 0.0000 712.5211 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 18.84328919765186 0 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 18.84328919765186 0 2.676236867904663 0.0 1 1 1 0 0.182740524411201 0.0 0.0 29253 7.21665132770771 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -153.0127 428285.7 713.5284 357.2678 238.5143 179.1376 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3" -33.237 510.2805 Cas7 KLLKVLK none 2 12.645284652709961 4 0.0 0 KLLKVLK 840.6161 0.0000 840.6161 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 18.84328919765186 0 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 18.84328919765186 0 2.676236867904663 0.0 1 1 1 0 0.182740524411201 0.0 0.0 29253 7.21665132770771 0 3.208958625793457 0.0 0.136603727936745 0.0 0.0 29253 8.896032099035239 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -88.9652 211160.6 841.6233 421.3153 281.2126 211.1613 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"LL-CO"|227.175506591796875,0.098765894770622,1,"LL"|242.18536376953125,0.01018890645355,1,"b2"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3" -33.791 717.3553 Cas7 VLKEDIAAIR U-H3O4P1 2 30.723300933837891 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 226.0590 1352.7300 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -39.9831 59026.7 1353.7373 677.3723 451.9173 339.1898 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" -33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 30.485282897949219 2 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" -33.791 717.3553 Cas7 EDIAAIR none 2 20.511859893798828 3 0.0 0 EDIAAIR 786.4236 0.0000 786.4236 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 7.072373390197754 0.0 0.099335506558418 0.0 0.0 29253 13.981020318661976 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -323.1363 819687.1 787.4308 394.2191 263.1485 197.6132 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"130.049942016601563,0.014329176396132,1,"b1"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|543.36065673828125,0.106723681092262,1,"y5"|658.3885498046875,0.117386691272259,1,"y6" -33.791 717.3553 Cas7 VLKEDIAAIR none 2 19.036767959594727 4 0.0 0 VLKEDIAAIR 1126.6710 0.0000 1126.6710 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 23.639501931617456 0 7.072373390197754 0.0 0.099335506558418 0.0 0.0 29253 13.981020318661976 0 9.227341651916504 0.0 1 1 1 0 0.158668205142021 0.0 0.0 29253 15.783117699886407 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -153.0126 271134.1 1127.6783 564.3428 376.5643 282.6750 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ 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1.844556570053101 184.46,126.75,97.82,0,0,32.15,32.15,0,0,0,0,0 mATSGMMTELGK 1255.5611 226.0590 1481.6200 19.278144836425781 14.91402530670166 1 1 1 0 0.371337056159973 4.102765560150146 0.158967092633247 29253 54.593068364401354 0 5.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -48.9889 66039.0 1482.6273 741.8173 494.8806 371.4123 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H2O1+"|953.44305419921875,0.880237638950348,1,"y9"|1036.4752197265625,0.154976740479469,1,"y10-H2O1+"|1037.4661865234375,0.044277537614107,1,"y10-H3N1+"|1054.489013671875,0.891642868518829,1,"y10"|1107.508056640625,0.010800593532622,1,"y11-H2O1+"|1125.5260009765625,0.135128006339073,1,"y11" -34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U-H2O1 2 32.330818176269531 1 0.536135375499725 0,0,0,53.61,0,0,0,0,6.09 MVFcLSAGK 970.4616 306.0253 1276.4869 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -9.0052 14087.1 1277.4942 639.2507 426.5029 320.1290 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O" -34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK UU-H2O1 2 31.977167129516602 2 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 612.0506 1582.5122 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 144.0075 -181767.2 1583.5195 792.2634 528.5114 396.6353 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U" -34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK none 2 21.468671798706055 3 0.0 0 MVFCLSAGK 970.4616 0.0000 970.4616 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 9.10000755455453 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -162.0178 333206.8 971.4689 486.2381 324.4945 243.6227 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U"120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|147.112640380859375,0.216315641999245,1,"y1"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5" -34.072 648.2559 Cse2 HQQALLRMVFCLSAGK none 2 16.85017204284668 4 0.0 0 HQQALLRMVFCLSAGK 1800.9491 0.0000 1800.9491 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 11.948224723472425 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 9.10000755455453 0 5.535978317260742 0.0 0.133406266570091 0.0 0.0 29253 7.792995663845979 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 253.2259 -280899.6 1801.9564 901.4818 601.3237 451.2446 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-36.767 933.9406 Cas7 TLALLSGKSVDEAEK U-H3O4P1 2 38.031223297119141 1 0.146051496267319 0,0,0,0,0,0,0,14.61,0,0,0,0,0,0,14.61 TLALLSGkSVDEAEk 1559.8407 226.0590 1785.8996 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 24.284693983617309 0 100.00 19.27 98.86 2.97 4.81 0.00 0.00 0.00 -39.9835 44726.4 1786.9069 893.9571 596.3072 447.4822 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ U'-H2O"|868.406494140625,0.043710377067328,1,"LSGKSVDE+C3O"|878.50921630859375,0.04271687194705,1,"b8+U'-H2O"|881.51123046875,0.10030597448349,1,"LALLSGK-CO+U-H3PO4"|997.42559814453125,0.045007601380348,1,"SGKSVDEAE+U'-H2O"|1056.4964599609375,0.445992678403854,1,"y9+U'-H2O"|1143.5274658203125,0.826412320137024,1,"y10+U'-H2O"|1179.6209716796875,0.033004622906446,1,"b11+U'-H2O"|1256.603515625,0.408009380102158,1,"y11+U'-H2O"|1369.7083740234375,0.034444786608219,1,"a14-H3N1+"|1440.7257080078125,0.081928692758083,1,"b12+U-H3PO4" -36.767 933.9406 Cas7 TLALLSGKSVDEAEK U-H2O1 2 37.87286376953125 2 0.146051496267319 0,0,0,0,0,0,0,14.61,0,0,0,0,0,0,14.61 TLALLSGkSVDEAEk 1559.8407 306.0253 1865.8660 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 24.284693983617309 0 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 24.284693983617309 0 100.00 19.27 98.86 2.97 4.81 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ U'-H2O"|868.406494140625,0.043710377067328,1,"LSGKSVDE+C3O"|878.50921630859375,0.04271687194705,1,"b8+U'-H2O"|881.51123046875,0.10030597448349,1,"LALLSGK-CO+U-H3PO4"|997.42559814453125,0.045007601380348,1,"SGKSVDEAE+U'-H2O"|1056.4964599609375,0.445992678403854,1,"y9+U'-H2O"|1143.5274658203125,0.826412320137024,1,"y10+U'-H2O"|1179.6209716796875,0.033004622906446,1,"b11+U'-H2O"|1256.603515625,0.408009380102158,1,"y11+U'-H2O"|1369.7083740234375,0.034444786608219,1,"a14-H3N1+"|1440.7257080078125,0.081928692758083,1,"b12+U-H3PO4"112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ U'-H2O"|868.406494140625,0.043710377067328,1,"LSGKSVDE+C3O"|878.50921630859375,0.04271687194705,1,"b8+U'-H2O"|881.51123046875,0.10030597448349,1,"LALLSGK-CO+U-H3PO4"|934.4134521484375,0.175290405750275,1,"a7+U-H2O"|997.42559814453125,0.045007601380348,1,"SGKSVDEAE+U'-H2O"|1056.4964599609375,0.445992678403854,1,"y9+U'-H2O"|1143.5274658203125,0.826412320137024,1,"y10+U'-H2O"|1179.6209716796875,0.033004622906446,1,"b11+U'-H2O"|1256.603515625,0.408009380102158,1,"y11+U'-H2O"|1369.7083740234375,0.034444786608219,1,"a14-H3N1+"|1440.7257080078125,0.081928692758083,1,"b12+U-H3PO4" -36.767 933.9406 Cas7 TLALLSGKSVDEAEK none 2 24.814916610717774 3 0.0 0 TLALLSGKSVDEAEK 1559.8407 0.0000 1559.8407 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 24.284693983617309 0 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 24.284693983617309 0 10.280866622924805 0.0 1 1 1 0 0.165740802884102 0.0 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-37.098 735.8139 Cse1 ALYTFAEGFK UU-H3O4P1 2 72.032722473144531 2 1.608833074569702 2.46,0,0,72.55,107.41,132.71,0,158.96,160.88,0 ALYTFAEGfK 1145.5757 532.0843 1677.6600 15.1768798828125 9.408187866210938 1 1 1 0 0.253406018018723 0.0 0.118536047637463 29253 34.900706116200745 0 15.1768798828125 9.408187866210938 1 1 1 0 0.253406018018723 0.0 0.118536047637463 29253 34.900706116200745 0 99.17 12.14 50.50 9.25 4.24 0.00 0.00 0.00 104.0234 -123861.3 1678.6673 839.8373 560.2273 420.4223 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U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" -39.118 623.2540 Cse2 MLTWWGK UU-H3O4P1 2 36.48870849609375 2 1.08866548538208 0,0.95,0,108.87,16.34,0,7.64 MLTwWGK 920.4578 532.0843 1452.5421 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 10.942926113371858 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 10.942926113371858 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 104.0244 -143032.4 1453.5494 727.2783 485.1880 364.1428 112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U"112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" -39.118 623.2540 Cas6e VPLIKEAEQIAWLQR none 2 17.291851043701172 3 0.0 0 VPLIKEAEQIAWLQR 1793.0200 0.0000 1793.0200 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 10.942926113371858 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 10.942926113371858 0 4.992705345153809 0.0 0.040718141943216 0.0 0.0 29253 10.942926113371858 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 274.2633 -305580.0 1794.0272 897.5173 598.6806 449.2623 112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U"112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ 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1 1 1 0 0.130456954240799 0.0 0.0 29253 7.778190140393486 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -153.0128 349541.2 874.4993 437.7533 292.1713 219.3803 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|147.112808227539063,0.358728766441345,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|431.26043701171875,0.208169266581535,1,"y4" +18.306 590.7661 Cas6e DLYQLHQGLWHLFPNR none 2 8.358111381530762 4 0.0 0 DLYQLHQGLWHLFPNR 2036.0381 0.0000 2036.0381 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.778190140393486 0 0.948040783405304 0.0 0.042552266269922 0.0 0.0 29253 5.328151996774687 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 428.2603 -420264.2 2037.0453 1019.0263 679.6866 510.0168 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|147.112808227539063,0.358728766441345,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|431.26043701171875,0.208169266581535,1,"y4"175.119796752929688,0.014619744382799,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|428.219207763671875,0.510025024414063,2,"LHQGLWH-H3N1++"|484.760772705078125,1.0,2,"LHQGLWHL-H3N1++"|520.25030517578125,0.025870239362121,1,"b4"|794.41949462890625,0.029359607025981,1,"LWHLFP"|855.42803955078125,0.362798720598221,1,"LHQGLWH-H3N1+" +25.116 508.1855 Cas5 YTPYLGR U-H3O4P1 3 30.759143829345703 1 0.637990474700928 0,0.24,0,63.80,0,0,0 YTPyLGR 868.4443 226.0590 1094.5033 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 24.764919939353597 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -142.3438 389085.8 1095.5106 548.2589 365.8417 274.6331 136.0615234375,1.0,1,"MI:A'"|136.07513427734375,0.229426234960556,1,"a1"|152.05633544921875,4.265095572918654e-03,1,"MI:G'"|158.092025756835938,9.572696872055531e-03,1,"y1-H3N1+"|164.070541381835938,3.483457025140524e-03,1,"b1"|175.119049072265625,0.031937755644321,1,"y1"|215.114288330078125,7.323490455746651e-03,1,"y2-H3N1+"|219.112014770507813,7.127284072339535e-03,1,"a2-H2O1+"|232.140228271484375,0.069322824478149,1,"y2"|237.123199462890625,0.195591405034065,1,"a2"|247.107315063476563,2.211090410128236e-03,1,"b2-H2O1+"|265.118011474609375,0.063581943511963,1,"b2"|285.1221923828125,7.153767161071301e-03,1,"PY-CO+C3O"|313.116943359375,3.152150195091963e-03,1,"PY+C3O"|327.1427001953125,1.970470184460282e-03,1,"PY-CO+U'-H2O"|328.198333740234375,2.614108612760902e-03,1,"y3-H3N1+"|329.17095947265625,0.072819426655769,2,"y5+C3O"|345.15252685546875,2.646437846124172e-03,1,"PY-CO+U'"|345.224029541015625,0.10897596180439,1,"y3"|348.06982421875,0.043133333325386,1,"MI:A"|359.1365966796875,2.3593760561198e-03,1,"b2+U'-H2O"|359.186859130859375,0.098186790943146,2,"y5+U'"|373.151611328125,2.350400667637587e-03,1,"PY+U'"|389.189697265625,2.83268908970058e-03,1,"YL+U'"|560.28369140625,0.03523913398385,1,"y4+C3O"|620.31134033203125,0.013985485769808,1,"b5-H2O1+"|657.33489990234375,0.3373843729496,1,"y5+C3O"|717.36590576171875,0.067729890346527,1,"y5+U'"|734.35107421875,3.099862718954682e-03,1,"y4+U-H3PO4"|758.38824462890625,0.013845652341843,1,"y6+C3O"|831.39337158203125,9.685350582003594e-03,1,"y5+U-H3PO4"|903.43212890625,2.896269550547004e-03,1,"[M+H-H2O]+ C3O"|921.44696044921875,0.019729314371943,1,"[M+H]+ C3O" +25.116 508.1855 Cas5 YTPYLGR U-H2O1 3 30.359920501708984 2 0.670666217803955 0,0.24,0,67.07,0,0,0 YTPyLGR 868.4443 306.0253 1174.4696 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 24.764919939353597 0 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 24.764919939353597 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -115.6884 294749.6 1175.4769 588.2421 392.4971 294.6247 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110.071525573730469,0.124598376452923,1,"iH+"|112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|204.134170532226563,0.047920491546392,1,"y2-C1H2N2+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|229.127822875976563,6.706117186695337e-03,1,"y2-H3N1+"|239.113800048828125,7.95002281665802e-03,1,"HT"|246.155319213867188,0.029895069077611,1,"y2"|286.150421142578125,0.037254326045513,1,"y3-H3N1+"|303.177154541015625,0.322829812765121,1,"y3"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|368.21673583984375,0.152305349707603,2,"y7-H2O1++"|377.221343994140625,0.194865599274635,2,"y7"|399.233306884765625,0.032629072666168,1,"y4-H3N1+"|415.200531005859375,0.011067586950958,1,"y3+U'"|416.16107177734375,9.909789077937603e-03,1,"b3"|416.2611083984375,0.390764862298965,1,"y4"|423.222259521484375,0.047973766922951,1,"TVLG+C3O"|477.163330078125,0.041644386947155,1,"a2+U-H3PO4"|499.19189453125,8.276323787868023e-03,1,"b4-H2O1+"|505.15753173828125,0.058943208307028,1,"b2+U-H3PO4"|510.177032470703125,9.497386403381825e-03,1,"b3+U'-H2O"|515.33038330078125,0.247247070074081,1,"y5"|517.205078125,0.010058866813779,1,"b4"|527.185791015625,0.053621523082256,1,"YH+U-H3PO4"|571.7821044921875,0.309090524911881,2,"y8+U-H3PO4"|598.37109375,0.028361488133669,1,"y6-H2O1+"|614.22186279296875,0.011790351010859,1,"a3+U-H3PO4"|616.3775634765625,0.524602711200714,1,"y6"|620.29071044921875,0.307169079780579,2,"[M+2H-H2O]++ U-H3PO4"|629.2969970703125,1.0,2,"[M+2H]++ U-H3PO4"|642.2138671875,0.065313711762428,1,"b3+U-H3PO4"|669.27935791015625,0.066578842699528,2,"[M+2H+U-H2O1]"|722.1842041015625,0.012603042647243,1,"b3+U-H2O"|735.421142578125,0.030300982296467,1,"y7-H2O1+"|743.26336669921875,0.047368142753839,1,"b4+U-H3PO4"|753.4393310546875,0.262213468551636,1,"y7"|814.327880859375,0.01301802136004,1,"HTVLG+U-H2O"|842.3365478515625,0.057222794741392,1,"b5+U-H3PO4"|898.3970947265625,0.025343561545014,1,"b7+U'"|909.42108154296875,0.010454332455993,1,"b8+C3O"|916.491455078125,0.011721312068403,1,"y8"|927.43896484375,0.037982285022736,1,"a6+U-H3PO4"|955.418212890625,0.050513833761215,1,"b6+U-H3PO4"|1031.5264892578125,0.180062636733055,1,"[M+H]+"|1083.4879150390625,0.025055043399334,1,"b8+U-H3PO4"|1143.546875,0.033915352076292,1,"[M+H]+ U'" +26.237 678.2844 Cas5 DYHTVLGAR U-H3O4P1 2 61.233551025390625 2 0.822381615638733 0,82.24,0,0,21.96,0,0,0,0 DyHTVLGAR 1030.5196 226.0590 1256.5786 12.389053344726563 10.107473373413086 1 1 1 0 0.218422010540962 4.155429840087891 0.046298556029797 29253 24.784701923534023 0 12.389053344726563 10.107473373413086 1 1 1 0 0.218422010540962 3.148078680038452 0.046298556029797 29253 24.784701923534023 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 -48.9879 77845.4 1257.5858 629.2966 419.8668 315.1519 110.071525573730469,0.124598376452923,1,"iH+"|112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|204.134170532226563,0.047920491546392,1,"y2-C1H2N2+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|229.127822875976563,6.706117186695337e-03,1,"y2-H3N1+"|239.113800048828125,7.95002281665802e-03,1,"HT"|246.155319213867188,0.029895069077611,1,"y2"|286.150421142578125,0.037254326045513,1,"y3-H3N1+"|303.177154541015625,0.322829812765121,1,"y3"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|368.21673583984375,0.152305349707603,2,"y7-H2O1++"|377.221343994140625,0.194865599274635,2,"y7"|399.233306884765625,0.032629072666168,1,"y4-H3N1+"|415.200531005859375,0.011067586950958,1,"y3+U'"|416.16107177734375,9.909789077937603e-03,1,"b3"|416.2611083984375,0.390764862298965,1,"y4"|423.222259521484375,0.047973766922951,1,"TVLG+C3O"|477.163330078125,0.041644386947155,1,"a2+U-H3PO4"|499.19189453125,8.276323787868023e-03,1,"b4-H2O1+"|505.15753173828125,0.058943208307028,1,"b2+U-H3PO4"|510.177032470703125,9.497386403381825e-03,1,"b3+U'-H2O"|515.33038330078125,0.247247070074081,1,"y5"|517.205078125,0.010058866813779,1,"b4"|527.185791015625,0.053621523082256,1,"YH+U-H3PO4"|571.7821044921875,0.309090524911881,2,"y8+U-H3PO4"|598.37109375,0.028361488133669,1,"y6-H2O1+"|614.22186279296875,0.011790351010859,1,"a3+U-H3PO4"|616.3775634765625,0.524602711200714,1,"y6"|620.29071044921875,0.307169079780579,2,"[M+2H-H2O]++ 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0.218422010540962 3.148078680038452 0.046298556029797 29253 24.784701923534023 0 12.389053344726563 0.0 1 1 1 0 0.218422010540962 0.0 0.0 29253 12.023569618634152 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 -162.0173 313824.7 1031.5269 516.2671 344.5138 258.6372 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+26.413 791.8590 Cse2 KSEQTTGISLGR U-H2O1 2 55.023689270019531 2 0.718522191047669 71.85,28.95,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 52.796759224531414 0 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 52.796759224531414 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 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U'-H2O"|685.85467529296875,1.0,2,"[M+2H]++ U'-H2O"|703.409912109375,0.085564941167831,1,"y7"|759.3389892578125,3.510346170514822e-03,1,"SEQTTGIS-CO-H3N1+"|769.3367919921875,3.813720541074872e-03,1,"SEQTTGI+C3O"|785.39312744140625,2.953411778435111e-03,1,"EQTTGISL-CO-H3N1+"|786.44580078125,3.075511427596211e-03,1,"y8-H2O1+"|804.4573974609375,0.129444718360901,1,"y8"|826.368896484375,7.392823696136475e-03,1,"b7+U'-H2O"|872.4322509765625,3.032000968232751e-03,1,"SEQTTGISL-CO-H3N1+"|873.38275146484375,8.629622869193554e-03,1,"a6+U-H3PO4"|911.447265625,9.337763302028179e-03,1,"EQTTGISLG-CO+C3O"|915.49517822265625,0.018657565116882,1,"y9-H3N1+"|932.51495361328125,0.120762772858143,1,"y9"|939.470703125,0.02140568383038,1,"b8+U'-H2O"|979.41162109375,9.381845593452454e-03,1,"QTTGISL-CO+U-H2O"|1026.4990234375,0.016941957175732,1,"b9+U'-H2O"|1043.5543212890625,0.036094401031733,1,"y10-H2O1+"|1045.54541015625,7.805424276739359e-03,1,"b10"|1061.558349609375,0.197863757610321,1,"y10"|1130.56640625,0.0313437320292,1,"y11-H2O1+"|1148.594970703125,0.08852231502533,1,"y11"|1158.5897216796875,0.020451299846172,1,"y9+U-H3PO4" +26.413 791.8590 Cse2 KSEQTTGISLGR none 2 31.117559432983398 3 0.0 0 KSEQTTGISLGR 1275.6783 0.0000 1275.6783 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 52.796759224531414 0 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 52.796759224531414 0 19.087356567382813 0.0 1 1 1 0 0.221869960427284 0.0 0.0 29253 27.420436422928944 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 -153.0126 239513.9 1276.6856 638.8464 426.2334 319.9268 112.050689697265625,9.990843944251537e-03,1,"MI:C'"|129.102371215820313,0.013408292084932,1,"b1"|136.061798095703125,0.902763903141022,1,"MI:A'"|136.074905395507813,0.051667388528585,1,"iK(C5H10N1)C3O"|152.056564331054688,3.377486718818545e-03,1,"MI:G'"|158.092697143554688,0.024075241759419,1,"y1-H3N1+"|175.118927001953125,0.081427209079266,1,"y1"|178.097412109375,0.341100573539734,1,"iK(C5H10N1)U'-H2O"|195.123382568359375,0.017177894711494,1,"a1+U'-H2O"|215.113723754882813,0.014229998923838,1,"y2-H3N1+"|227.066909790039063,0.016493165865541,1,"MI:U-H3PO4"|232.140274047851563,0.180095225572586,1,"y2"|241.1295166015625,0.01908091455698,1,"b1+U'"|258.143798828125,3.849325468763709e-03,1,"GIS"|282.156463623046875,0.019274268299341,1,"a2+U'-H2O"|310.150787353515625,0.118582129478455,1,"b2+U'-H2O"|327.212188720703125,3.42642655596137e-03,1,"y3-H2O1+"|328.199676513671875,4.501644056290388e-03,1,"y3-H3N1+"|345.223907470703125,0.247861370444298,1,"y3"|348.0692138671875,7.973242551088333e-03,1,"MI:A"|428.180908203125,8.386147208511829e-03,1,"SEQT-H2O1+"|432.25604248046875,0.183289110660553,1,"y4"|439.19366455078125,0.044542569667101,1,"b3+U'-H2O"|517.22088623046875,3.666676813736558e-03,1,"EQTTG"|529.219970703125,9.659912437200546e-03,1,"SEQTT-H2O1+"|545.3385009765625,0.023281643167138,1,"TTGISL-CO"|567.25286865234375,0.052726376801729,1,"b4+U'-H2O"|602.3612060546875,0.080439247190952,1,"TTGISLG-CO"|676.849365234375,0.461511492729187,2,"[M+2H-H2O]++ 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112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" +33.237 510.2805 Cas7 LLKVLK none 2 13.002236366271973 3 0.0 0 LLKVLK 712.5211 0.0000 712.5211 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 25.626236396593821 0 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 25.626236396593821 0 2.676236867904663 0.0 1 1 1 0 0.182740524411201 0.0 0.0 29253 7.604012361908893 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -153.0127 428285.7 713.5284 357.2678 238.5143 179.1376 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3" +33.237 510.2805 Cas7 KLLKVLK none 2 12.645284652709961 4 0.0 0 KLLKVLK 840.6161 0.0000 840.6161 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 25.626236396593821 0 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 25.626236396593821 0 2.676236867904663 0.0 1 1 1 0 0.182740524411201 0.0 0.0 29253 7.604012361908893 0 3.208958625793457 0.0 0.136603727936745 0.0 0.0 29253 10.229427823002553 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -88.9652 211160.6 841.6233 421.3153 281.2126 211.1613 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"LL-CO"|227.175506591796875,0.098765894770622,1,"LL"|242.18536376953125,0.01018890645355,1,"b2"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3" +33.791 717.3553 Cas7 VLKEDIAAIR U-H3O4P1 2 30.723300933837891 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 226.0590 1352.7300 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -39.9831 59026.7 1353.7373 677.3723 451.9173 339.1898 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" +33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 30.485282897949219 2 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" +33.791 717.3553 Cas7 EDIAAIR none 2 20.511859893798828 3 0.0 0 EDIAAIR 786.4236 0.0000 786.4236 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 7.072373390197754 0.0 0.099335506558418 0.0 0.0 29253 10.246214303295313 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -323.1363 819687.1 787.4308 394.2191 263.1485 197.6132 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"130.049942016601563,0.014329176396132,1,"b1"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|543.36065673828125,0.106723681092262,1,"y5"|658.3885498046875,0.117386691272259,1,"y6" +33.791 717.3553 Cas7 VLKEDIAAIR none 2 19.036767959594727 4 0.0 0 VLKEDIAAIR 1126.6710 0.0000 1126.6710 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 7.072373390197754 0.0 0.099335506558418 0.0 0.0 29253 10.246214303295313 0 9.227341651916504 0.0 1 1 1 0 0.158668205142021 0.0 0.0 29253 10.246214303295313 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -153.0126 271134.1 1127.6783 564.3428 376.5643 282.6750 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ 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1.844556570053101 184.46,126.75,97.82,0,0,32.15,32.15,0,0,0,0,0 mATSGMMTELGK 1255.5611 226.0590 1481.6200 19.278144836425781 14.91402530670166 1 1 1 0 0.371337056159973 4.102765560150146 0.158967092633247 29253 47.324498821223671 0 5.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -48.9889 66039.0 1482.6273 741.8173 494.8806 371.4123 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H2O1+"|953.44305419921875,0.880237638950348,1,"y9"|1036.4752197265625,0.154976740479469,1,"y10-H2O1+"|1037.4661865234375,0.044277537614107,1,"y10-H3N1+"|1054.489013671875,0.891642868518829,1,"y10"|1107.508056640625,0.010800593532622,1,"y11-H2O1+"|1125.5260009765625,0.135128006339073,1,"y11" +34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U-H2O1 2 32.330818176269531 1 0.536135375499725 0,0,0,53.61,0,0,0,0,6.09 MVFcLSAGK 970.4616 306.0253 1276.4869 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -9.0052 14087.1 1277.4942 639.2507 426.5029 320.1290 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O" +34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK UU-H2O1 2 31.977167129516602 2 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 612.0506 1582.5122 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 144.0075 -181767.2 1583.5195 792.2634 528.5114 396.6353 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U" +34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK none 2 21.468671798706055 3 0.0 0 MVFCLSAGK 970.4616 0.0000 970.4616 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 7.007274678147403 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -162.0178 333206.8 971.4689 486.2381 324.4945 243.6227 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U"120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|147.112640380859375,0.216315641999245,1,"y1"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5" +34.072 648.2559 Cse2 HQQALLRMVFCLSAGK none 2 16.85017204284668 4 0.0 0 HQQALLRMVFCLSAGK 1800.9491 0.0000 1800.9491 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 7.007274678147403 0 5.535978317260742 0.0 0.133406266570091 0.0 0.0 29253 5.499638206201645 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 253.2259 -280899.6 1801.9564 901.4818 601.3237 451.2446 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+36.767 933.9406 Cas7 TLALLSGKSVDEAEK U-H3O4P1 2 38.031223297119141 1 0.146051496267319 0,0,0,0,0,0,0,14.61,0,0,0,0,0,0,14.61 TLALLSGkSVDEAEk 1559.8407 226.0590 1785.8996 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 30.20450085062139 0 100.00 19.27 98.86 2.97 4.81 0.00 0.00 0.00 -39.9835 44726.4 1786.9069 893.9571 596.3072 447.4822 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ 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0.4 1866.8732 933.9403 622.9626 467.4738 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ 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U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" +39.118 623.2540 Cse2 MLTWWGK UU-H3O4P1 2 36.48870849609375 2 1.08866548538208 0,0.95,0,108.87,16.34,0,7.64 MLTwWGK 920.4578 532.0843 1452.5421 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 104.0244 -143032.4 1453.5494 727.2783 485.1880 364.1428 112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U"112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" +39.118 623.2540 Cas6e VPLIKEAEQIAWLQR none 2 17.291851043701172 3 0.0 0 VPLIKEAEQIAWLQR 1793.0200 0.0000 1793.0200 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 4.992705345153809 0.0 0.040718141943216 0.0 0.0 29253 8.25391312848474 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 274.2633 -305580.0 1794.0272 897.5173 598.6806 449.2623 112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U"112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ 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diff --git a/src/topp/OpenNuXL.cpp b/src/topp/OpenNuXL.cpp index 98bfdfa1acb..e1bfa7688fa 100644 --- a/src/topp/OpenNuXL.cpp +++ b/src/topp/OpenNuXL.cpp @@ -420,8 +420,6 @@ struct NuXLRTPrediction map encodeAAHist_(const AASequence& aa_seq) { - const String& seq = aa_seq.toUnmodifiedString(); - map v; for (auto& c : aa_seq) { @@ -1383,35 +1381,29 @@ class OpenNuXL : // determine b+a and y-ion count UInt y_ion_count(0), b_ion_count(0), a_ion_count(0); - double b_sum(0.0); for (Size i = 0; i != b_ions.size(); ++i) { if (b_ions[i] > 0) { intensity_sum[i] += b_ions[i]; - b_sum += b_ions[i]; ++b_ion_count; } } - double y_sum(0.0); for (Size i = 0; i != y_ions.size(); ++i) { if (y_ions[i] > 0) { intensity_sum[i] += y_ions[i]; - y_sum += y_ions[i]; ++y_ion_count; } } - double a_sum(0.0); for (Size i = 0; i != a_ions.size(); ++i) { if (a_ions[i] > 0) { intensity_sum[i] += a_ions[i]; - a_sum += a_ions[i]; ++a_ion_count; } } @@ -1437,7 +1429,7 @@ class OpenNuXL : MIC = std::accumulate(intensity_sum.begin(), intensity_sum.end(), 0.0); for (auto& i : intensity_sum) { i /= TIC; } // scale intensity sum MIC /= TIC; - Morph = b_ion_count + y_ion_count + y_ion_count + MIC; + Morph = b_ion_count + y_ion_count + MIC; err = (y_mean_err + b_mean_err)/(b_ion_count + y_ion_count); } @@ -2446,17 +2438,6 @@ static void scoreXLIons_( } std::sort(matched_ranks.begin(), matched_ranks.end()); - // optimal ranking would be 0,1, ... , (number_of_matched_peaks - 1) - // calculate number of "insertions" of higher-intensity peaks compared to optimal ranking - size_t sum_rank_diff(matched_ranks[0]); - for (size_t i = 1; i != matched_ranks.size(); ++i) - { - sum_rank_diff += matched_ranks[i] - matched_ranks[0] - 1; - } -///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - //r.wTop50 = log10(1.0 + sum_rank_diff); -///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - double avg_int{}; size_t n_unexplained_greater_avg{}; for (size_t i = 0; i != spectrum.size(); ++i) @@ -5056,7 +5037,7 @@ static void scoreXLIons_( { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "q-value list for PSMs and peptides differ in size.", - String(XL_FDR.size() + "!=" + XL_peptidelevel_FDR.size())); + String(XL_FDR.size()) + "!=" + String(XL_peptidelevel_FDR.size())); } // determine maximum FDR treshold used to create result files From cb49f3163dd175f66054303bcf236d988ea8305c Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 23 Jan 2025 11:43:19 +0100 Subject: [PATCH 325/471] more consistent ion charge format --- .../ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp | 17 +- .../NUXL/NuXLFragmentAnnotationHelper.cpp | 7 +- src/tests/topp/OpenNuXL_1_output.idXML | 42 ++--- src/tests/topp/OpenNuXL_2_output.idXML | 42 ++--- src/tests/topp/OpenNuXL_3_output.idXML | 54 +++--- src/tests/topp/OpenNuXL_3_output2.tsv | 52 +++--- src/tests/topp/OpenNuXL_4_output.idXML | 52 +++--- src/tests/topp/OpenNuXL_4_output2.tsv | 50 +++--- src/tests/topp/OpenNuXL_5_output.idXML | 42 ++--- src/tests/topp/OpenNuXL_6_output.idXML | 158 ++++++++--------- src/tests/topp/OpenNuXL_6_output2.tsv | 160 +++++++++--------- 11 files changed, 341 insertions(+), 335 deletions(-) diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp index 1167bff6388..19bb64501a7 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp @@ -18,6 +18,8 @@ #include // for OPENMS_PRECONDITION #include +#include + using namespace std; //#define DEBUG_OpenNuXL @@ -25,6 +27,8 @@ using namespace std; namespace OpenMS { + static const std::regex trailing_charge_pattern_rx(R"(\++$)"); // match one or more '+' characters at the end of the string + // create total loss spectrum using new_param as template static PeakSpectrum createTotalLossSpectrumForAnnotations(const AASequence& fixed_and_variable_modified_peptide, size_t precursor_charge, Param new_param) { @@ -544,7 +548,7 @@ namespace OpenMS fa.mz = fragment_mz; fa.intensity = fragment_intensity; fa.charge = 1; - fa.annotation = ion_name; + fa.annotation = ion_name + "+"; annotated_marker_ions.push_back(fa); } else @@ -561,7 +565,7 @@ namespace OpenMS fa.mz = fragment_mz; fa.intensity = fragment_intensity; fa.charge = 1; - fa.annotation = ion_name; + fa.annotation = ion_name + "+"; shifted_immonium_ions.push_back(fa); } else @@ -575,7 +579,10 @@ namespace OpenMS fa.mz = fragment_mz; fa.intensity = fragment_intensity; fa.charge = charge; - fa.annotation = ion_name; + static const std::regex pattern(R"(\](\++)+)"); + fa.annotation = std::regex_replace(ion_name, pattern, "]"); // remove charge inside string (e.g., before loss) + fa.annotation.substitute(' ', '+'); // turn gap into plus "[M+2H] U-H2O" -> "[M+2H]+U-H2O" + fa.annotation += String(charge, '+'); // add charges back at end annotated_precursor_ions.push_back(fa); } else if (isupper(ion_name[0])) // shifted internal ions @@ -585,8 +592,8 @@ namespace OpenMS fa.intensity = fragment_intensity; fa.charge = charge; String with_plus = ion_name; - with_plus.substitute(' ', '+'); - fa.annotation = with_plus; // turn "PEPT U-H2O" into "PEPT+U-H20" + with_plus.substitute(' ', '+'); // turn "PEPT U-H2O" into "PEPT+U-H20" + fa.annotation = with_plus + String(charge, '+'); shifted_immonium_ions.push_back(fa); //TODO: add to shifted_internal_fragment_ions or rename vector } } diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLFragmentAnnotationHelper.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLFragmentAnnotationHelper.cpp index c401bd906ec..9fff565d1d1 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLFragmentAnnotationHelper.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLFragmentAnnotationHelper.cpp @@ -23,7 +23,7 @@ namespace OpenMS { String NuXLFragmentAnnotationHelper::getAnnotatedImmoniumIon(char c, const String& fragment_shift_name) { - return String("i") + c + "+" + fragment_shift_name; + return String("i") + c + "+" + fragment_shift_name + "+"; } std::vector NuXLFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA( @@ -41,11 +41,11 @@ namespace OpenMS fa.intensity = sit.intensity; if (sit.shift.empty()) { - fa.annotation = ion_type + String(ait.first); + fa.annotation = ion_type + String(ait.first) + String(fa.charge, '+'); } else { - const String annotation_text = ion_type + String(ait.first) + "+" + sit.shift; + const String annotation_text = ion_type + String(ait.first) + "+" + sit.shift + String(fa.charge, '+'); fa.annotation = annotation_text; } fas.push_back(std::move(fa)); @@ -75,7 +75,6 @@ namespace OpenMS return fas; } - String NuXLFragmentAnnotationHelper::shiftedIonsToString(const std::vector& as) { std::vector sorted(as); diff --git a/src/tests/topp/OpenNuXL_1_output.idXML b/src/tests/topp/OpenNuXL_1_output.idXML index b925a3fc4e6..ace5a147fb7 100644 --- a/src/tests/topp/OpenNuXL_1_output.idXML +++ b/src/tests/topp/OpenNuXL_1_output.idXML @@ -6,7 +6,7 @@ - + @@ -32,7 +32,7 @@ - + @@ -112,7 +112,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -272,7 +272,7 @@ - + @@ -352,7 +352,7 @@ - + @@ -432,7 +432,7 @@ - + @@ -512,7 +512,7 @@ - + @@ -592,7 +592,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -752,7 +752,7 @@ - + @@ -832,7 +832,7 @@ - + @@ -912,7 +912,7 @@ - + @@ -992,7 +992,7 @@ - + @@ -1072,7 +1072,7 @@ - + @@ -1152,7 +1152,7 @@ - + @@ -1232,7 +1232,7 @@ - + @@ -1312,7 +1312,7 @@ - + @@ -1392,7 +1392,7 @@ - + @@ -1472,7 +1472,7 @@ - + @@ -1552,7 +1552,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_2_output.idXML b/src/tests/topp/OpenNuXL_2_output.idXML index adfd69aea78..cb531638ad2 100644 --- a/src/tests/topp/OpenNuXL_2_output.idXML +++ b/src/tests/topp/OpenNuXL_2_output.idXML @@ -6,7 +6,7 @@ - + @@ -32,7 +32,7 @@ - + @@ -112,7 +112,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -272,7 +272,7 @@ - + @@ -352,7 +352,7 @@ - + @@ -432,7 +432,7 @@ - + @@ -512,7 +512,7 @@ - + @@ -592,7 +592,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -752,7 +752,7 @@ - + @@ -832,7 +832,7 @@ - + @@ -912,7 +912,7 @@ - + @@ -992,7 +992,7 @@ - + @@ -1072,7 +1072,7 @@ - + @@ -1152,7 +1152,7 @@ - + @@ -1232,7 +1232,7 @@ - + @@ -1312,7 +1312,7 @@ - + @@ -1392,7 +1392,7 @@ - + @@ -1472,7 +1472,7 @@ - + @@ -1552,7 +1552,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_3_output.idXML b/src/tests/topp/OpenNuXL_3_output.idXML index 235b10dca13..47c5e988a6d 100644 --- a/src/tests/topp/OpenNuXL_3_output.idXML +++ b/src/tests/topp/OpenNuXL_3_output.idXML @@ -6,7 +6,7 @@ - + @@ -44,7 +44,7 @@ - + @@ -124,7 +124,7 @@ - + @@ -204,7 +204,7 @@ - + @@ -284,7 +284,7 @@ - + @@ -364,7 +364,7 @@ - + @@ -444,7 +444,7 @@ - + @@ -520,7 +520,7 @@ - + @@ -596,7 +596,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -748,7 +748,7 @@ - + @@ -824,7 +824,7 @@ - + @@ -896,7 +896,7 @@ - + @@ -976,7 +976,7 @@ - + @@ -1052,7 +1052,7 @@ - + @@ -1128,7 +1128,7 @@ - + @@ -1208,7 +1208,7 @@ - + @@ -1288,7 +1288,7 @@ - + @@ -1368,7 +1368,7 @@ - + @@ -1448,7 +1448,7 @@ - + @@ -1528,7 +1528,7 @@ - + @@ -1608,7 +1608,7 @@ - + @@ -1688,7 +1688,7 @@ - + @@ -1764,7 +1764,7 @@ - + @@ -1840,7 +1840,7 @@ - + @@ -1920,7 +1920,7 @@ - + @@ -2000,7 +2000,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_3_output2.tsv b/src/tests/topp/OpenNuXL_3_output2.tsv index d3aa37d250b..37c9406d0e4 100644 --- a/src/tests/topp/OpenNuXL_3_output2.tsv +++ b/src/tests/topp/OpenNuXL_3_output2.tsv @@ -1,27 +1,27 @@ #RT m/z proteins peptide NA charge score rank best localization score localization scores best localization(s) peptide weight NA weight cross-link weight NuXL:total_loss_score NuXL:partial_loss_score CountSequenceIsTop CountSequenceCharges CountSequenceIsXL CountSequenceIsPeptide NuXL:MIC NuXL:pl_pc_MIC NuXL:pl_MIC nr_candidates -ln(poisson) isotope_error A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H fragment_annotation -17.788 712.7828 Cas7 AEADNLDDKK U-H2O1 2 69.974990844726563 1 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 306.0253 1423.5504 11.444543838500977 16.099458694458008 1 1 1 0 0.216474175453186 0.0 0.394327819347382 3 315.0 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 112.050621032714844,0.028104400262237,1,"MI:C'"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O"|501.19091796875,0.035030111670494,1,"b5"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O"|584.267578125,9.894491173326969e-03,1,"LDDK+U'"|586.28167724609375,0.011093857698143,1,"a6"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]++ U'-H2O"|599.27777099609375,0.764611601829529,1,"y4+U'-H2O"|606.77734375,0.299497008323669,2,"[M+2H]++ U'-H2O"|614.27984619140625,0.039939478039742,1,"b6"|680.2978515625,0.018134105950594,1,"a6+U'-H2O"|698.31036376953125,6.59028347581625e-03,1,"LDDK+U-H3PO4"|712.36236572265625,0.394213527441025,1,"y5+U'-H2O"|729.31292724609375,6.610926240682602e-03,1,"b7"|795.32373046875,0.023242574185133,1,"a7+U'-H2O"|826.40509033203125,0.400069534778595,1,"y6+U'-H2O"|844.32489013671875,6.451499182730913e-03,1,"b8"|866.3614501953125,0.062791705131531,1,"ADNLDDK+U'-H2O"|884.37408447265625,7.893706671893597e-03,1,"EADNLDDK-H3N1+"|941.43206787109375,0.44364058971405,1,"y7+U'-H2O"|1012.468994140625,0.708723366260529,1,"y8+U'-H2O"|1066.4478759765625,0.035385373979807,1,"b9+U'-H2O"|1141.5120849609375,7.319674827158451e-03,1,"y9+U'-H2O"|1212.5546875,0.066727869212627,1,"[M+H]+ U'-H2O" -18.306 590.7661 Cas6e LDSKGNIK U-H2O1 2 25.741664886474609 1 2.196093797683716 0,0,0,219.61,0,0,0,8.00 LDSkGNIK 873.4920 306.0253 1179.5173 2.428377628326416 4.320775508880615 1 1 1 0 0.130456954240799 0.0 0.175812318921089 1 315.0 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O" -25.116 508.1855 Cas5 YTPYLGR AU 3 40.562583923339844 1 0.734427034854889 0,0.24,0,73.44,0,0,0 YTPyLGR 868.4443 653.0884 1521.5327 3.710045576095581 2.351816177368164 1 1 1 0 0.190965637564659 0.0 0.210292190313339 1 315.0 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 136.0615234375,1.0,1,"MI:A'"|136.07513427734375,0.229426234960556,1,"a1"|152.05633544921875,4.265095572918654e-03,1,"MI:G'"|158.092025756835938,9.572696872055531e-03,1,"y1-H3N1+"|164.070541381835938,3.483457025140524e-03,1,"b1"|175.119049072265625,0.031937755644321,1,"y1"|215.114288330078125,7.323490455746651e-03,1,"y2-H3N1+"|219.112014770507813,7.127284072339535e-03,1,"a2-H2O1+"|232.140228271484375,0.069322824478149,1,"y2"|237.123199462890625,0.195591405034065,1,"a2"|247.107315063476563,2.211090410128236e-03,1,"b2-H2O1+"|265.118011474609375,0.063581943511963,1,"b2"|285.1221923828125,7.153767161071301e-03,1,"PY-CO+C3O"|313.116943359375,3.152150195091963e-03,1,"PY+C3O"|327.1427001953125,1.970470184460282e-03,1,"PY-CO+U'-H2O"|328.198333740234375,2.614108612760902e-03,1,"y3-H3N1+"|329.17095947265625,0.072819426655769,2,"y5+C3O"|345.15252685546875,2.646437846124172e-03,1,"PY-CO+U'"|345.224029541015625,0.10897596180439,1,"y3"|348.06982421875,0.043133333325386,1,"MI:A"|359.1365966796875,2.3593760561198e-03,1,"b2+U'-H2O"|359.186859130859375,0.098186790943146,2,"y5+U'"|373.151611328125,2.350400667637587e-03,1,"PY+U'"|389.189697265625,2.83268908970058e-03,1,"YL+U'"|456.184844970703125,0.019872423261404,2,"y5+U-H2O"|465.191619873046875,0.025686334818602,2,"y5+U"|560.28369140625,0.03523913398385,1,"y4+C3O"|620.31134033203125,0.013985485769808,1,"b5-H2O1+"|657.33489990234375,0.3373843729496,1,"y5+C3O"|717.36590576171875,0.067729890346527,1,"y5+U'"|734.35107421875,3.099862718954682e-03,1,"y4+U-H3PO4"|758.38824462890625,0.013845652341843,1,"y6+C3O"|831.39337158203125,9.685350582003594e-03,1,"y5+U-H3PO4"|849.408447265625,4.016013350337744e-03,1,"y5+U-HPO3"|903.43212890625,2.896269550547004e-03,1,"[M+H-H2O]+ C3O"|911.36871337890625,0.012803317978978,1,"y5+U-H2O"|921.44696044921875,0.019729314371943,1,"[M+H]+ C3O"|929.37530517578125,0.034058455377817,1,"y5+U" -26.237 678.2844 Cas5 DYHTVLGAR U 2 67.563796997070313 1 0.892229020595551 0,89.22,0,0,23.58,0,0,0,0 DyHTVLGAR 1030.5196 324.0359 1354.5555 12.389053344726563 8.871867179870606 1 1 1 0 0.218422010540962 0.0 0.070792749524117 3 315.0 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 110.071525573730469,0.124598376452923,1,"iH+"|112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|204.134170532226563,0.047920491546392,1,"y2-C1H2N2+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|229.127822875976563,6.706117186695337e-03,1,"y2-H3N1+"|239.113800048828125,7.95002281665802e-03,1,"HT"|246.155319213867188,0.029895069077611,1,"y2"|286.150421142578125,0.037254326045513,1,"y3-H3N1+"|303.177154541015625,0.322829812765121,1,"y3"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|368.21673583984375,0.152305349707603,2,"y7-H2O1++"|377.221343994140625,0.194865599274635,2,"y7"|399.233306884765625,0.032629072666168,1,"y4-H3N1+"|415.200531005859375,0.011067586950958,1,"y3+U'"|416.16107177734375,9.909789077937603e-03,1,"b3"|416.2611083984375,0.390764862298965,1,"y4"|423.222259521484375,0.047973766922951,1,"TVLG+C3O"|477.163330078125,0.041644386947155,1,"a2+U-H3PO4"|499.19189453125,8.276323787868023e-03,1,"b4-H2O1+"|505.15753173828125,0.058943208307028,1,"b2+U-H3PO4"|510.177032470703125,9.497386403381825e-03,1,"b3+U'-H2O"|515.33038330078125,0.247247070074081,1,"y5"|517.205078125,0.010058866813779,1,"b4"|527.185791015625,0.053621523082256,1,"YH+U-H3PO4"|571.7821044921875,0.309090524911881,2,"y8+U-H3PO4"|598.37109375,0.028361488133669,1,"y6-H2O1+"|614.22186279296875,0.011790351010859,1,"a3+U-H3PO4"|616.3775634765625,0.524602711200714,1,"y6"|620.29071044921875,0.307169079780579,2,"[M+2H-H2O]++ 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KSEQTTGISLGR U-H2O1 2 59.922630310058594 1 0.718522191047669 71.85,28.95,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 19.087356567382813 10.870758056640625 1 1 1 0 0.221869960427284 0.0 0.115903504192829 2 315.0 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 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U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"b4+C3O"|548.35498046875,0.371608823537827,1,"KLLV+U'-H2O"|562.3695068359375,0.036407515406609,1,"b4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" -33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 31.678943634033203 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 0.0 0.059569962322712 2 315.0 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ 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127.086746215820313,0.03221358731389,1,"a2-C1H4S1+"|129.102340698242188,0.159227415919304,1,"y1-H2O1+"|130.086349487304688,0.051548503339291,1,"y1-H3N1+"|136.061599731445313,0.055803153663874,1,"MI:A'"|147.1126708984375,0.148163199424744,1,"y1"|155.081497192382813,0.034486405551434,1,"b2-C1H4S1+"|161.09222412109375,0.014802157878876,1,"TS-CO"|171.076675415039063,0.03485019877553,1,"TS-H2O1+"|173.092819213867188,0.028763445094228,1,"AT"|175.087371826171875,0.010726612992585,1,"a2"|186.123825073242188,0.109146893024445,1,"y2-H2O1+"|187.108383178710938,0.012273258529603,1,"y2-H3N1+"|189.0869140625,0.018883759155869,1,"TS"|204.134185791015625,0.664878964424133,1,"y2"|215.083221435546875,0.011490193195641,1,"MM-C1H4S1+"|216.079666137695313,0.14799277484417,1,"a1+U'"|228.098098754882813,0.016218513250351,1,"SGM-C1H4S1+"|228.134857177734375,0.010106886737049,1,"a3-C1H4S1+"|231.098358154296875,0.02963631041348,1,"TE"|233.09527587890625,0.010079103522003,1,"MT"|241.0823974609375,0.03026669844985,1,"TS+C3O"|256.129425048828125,0.036421522498131,1,"b3-C1H4S1+"|275.06927490234375,0.321486562490463,1,"iM+U-H3PO4"|287.116729736328125,0.106576167047024,1,"a2+U'"|315.11212158203125,0.182710662484169,1,"b2+U'"|317.21807861328125,0.5060915350914,1,"y3"|330.111419677734375,0.107610121369362,1,"a1+U-H3PO4"|344.18218994140625,0.014792915433645,1,"TEL"|362.13836669921875,0.03236985206604,1,"MTE"|373.04638671875,0.055028561502695,1,"iM+U"|398.15032958984375,0.053473096340895,1,"b3+U'-H2O"|401.148590087890625,0.368163228034973,1,"TSGM-CO+C3O"|401.2054443359375,0.016921009868383,1,"TELG"|416.1590576171875,0.204516366124153,1,"b3+U'"|421.157745361328125,0.010915133170784,1,"GMMT"|428.089111328125,0.018594333902001,1,"a1+U"|428.249847412109375,0.052017502486706,1,"y4-H2O1+"|429.14337158203125,0.84875214099884,1,"TSGM+C3O"|446.26116943359375,0.214159980416298,1,"y4"|475.222991943359375,0.012469680979848,1,"MTEL"|485.180511474609375,0.03207815811038,1,"b4+U'-H2O"|490.177520751953125,0.032220557332039,1,"TSGMM-H2O1+"|508.19189453125,0.012716436758637,1,"TSGMM"|529.29425048828125,0.015442945063114,1,"y5-H2O1+"|530.19122314453125,0.180141240358353,1,"b3+U-H3PO4"|532.1845703125,0.013560008257627,1,"GMMTE-H2O1+"|542.2000732421875,0.010952124372125,1,"b5+U'-H2O"|547.30767822265625,0.328858405351639,1,"y5"|550.20074462890625,0.012767584063113,1,"GMMTE"|587.2828369140625,0.01402248814702,1,"GMMTEL-CO-C1H4S1+"|589.23138427734375,0.013000959530473,1,"SGMMTE-C1H4S1+"|604.78570556640625,0.331091970205307,2,"[M+2H]-CH4S"|619.224365234375,0.037525855004787,1,"SGMMTE-H2O1+"|631.2183837890625,0.011294193565845,1,"b6+C3O"|637.2349853515625,0.038924634456635,1,"SGMMTE"|645.2703857421875,0.017423829063773,1,"GMMTEL-H2O1+"|663.287109375,0.01368575822562,1,"GMMTEL"|673.23809814453125,0.050370126962662,1,"b6+U'-H2O"|675.79296875,0.031400952488184,2,"[M+2H]++ U'-H2O"|678.34820556640625,0.334554493427277,1,"y6"|720.27740478515625,0.039541512727737,1,"TSGMMTE-H2O1+"|732.30474853515625,0.01200485881418,1,"SGMMTEL-H2O1+"|732.81005859375,0.290660262107849,2,"[M+2H-H2O]++ U-H3PO4"|738.28192138671875,0.013668600469828,1,"TSGMMTE"|741.81646728515625,1.0,2,"[M+2H]++ U-H3PO4"|750.3192138671875,0.014047367498279,1,"SGMMTEL"|777.29205322265625,0.015259876847267,1,"a6+U-H3PO4"|805.287353515625,0.180637359619141,1,"b6+U-H3PO4"|809.39007568359375,0.169192254543304,1,"y7"|833.35845947265625,0.018561428412795,1,"TSGMMTEL-H2O1+"|851.35504150390625,0.011303779669106,1,"TSGMMTEL"|866.41046142578125,0.621590375900269,1,"y8"|935.43035888671875,0.04818819090724,1,"y9-H2O1+"|936.31427001953125,0.07395213842392,1,"b7+U-H3PO4"|953.44305419921875,0.880237638950348,1,"y9"|1036.4752197265625,0.154976740479469,1,"y10-H2O1+"|1037.4661865234375,0.044277537614107,1,"y10-H3N1+"|1054.489013671875,0.891642868518829,1,"y10"|1107.508056640625,0.010800593532622,1,"y11-H2O1+"|1125.5260009765625,0.135128006339073,1,"y11"|1166.414794921875,0.100423000752926,1,"b9+U-H3PO4"|1279.4962158203125,0.065082639455795,1,"b10+U-H3PO4"|1308.5689697265625,0.035434119403362,1,"[M+H]+ C3O" -34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U 2 37.691276550292969 1 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 324.0359 1294.4975 6.533727645874023 1.259999871253967 1 1 1 0 0.223560705780983 0.0 0.098648108541965 2 315.0 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U" -36.528 938.3693 Cas7 DDMNMQKDAIFGGK U-H2O1 2 45.990291595458984 1 1.136792063713074 0,0,0,0,0,0,113.68,0,0,0,0,0,0,11.93 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 14.737911224365234 7.284058094024658 1 1 1 0 0.299404740333557 0.0 0.158554673194885 1 315.0 0 60.88 11.73 11.30 0.00 6.83 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 112.050605773925781,0.113011009991169,1,"MI:C'"|120.08087158203125,0.052033305168152,1,"iF+"|129.10211181640625,0.21279302239418,1,"y1-H2O1+"|130.086380004882813,0.07728461176157,1,"y1-H3N1+"|136.061721801757813,0.608757317066193,1,"MI:A'"|147.112777709960938,0.152066215872765,1,"y1"|152.056549072265625,0.068255327641964,1,"MI:G'"|178.096817016601563,0.119268953800201,1,"iK(C5H10N1)U'-H2O"|186.123748779296875,0.069755658507347,1,"y2-H2O1+"|204.133987426757813,0.293571650981903,1,"y2"|227.06640625,0.015322148799896,1,"MI:U-H3PO4"|231.061355590820313,0.064788468182087,1,"b2"|243.144866943359375,0.019257104024291,1,"y3-H2O1+"|246.090835571289063,0.09425338357687,1,"MN"|261.1553955078125,0.74517822265625,1,"y3"|338.144195556640625,0.02742194198072,1,"KD+U'-H2O"|344.14312744140625,0.023650586605072,1,"MQ-CO+U'"|348.07073974609375,0.025085339322686,1,"MI:A"|362.098541259765625,0.09182520955801,1,"b3"|408.223114013671875,1.0,1,"y4"|431.12469482421875,0.016397748142481,1,"a4-H3N1+"|476.143310546875,0.111722677946091,1,"b4"|494.268829345703125,0.014951772987843,1,"KDAI-CO+U'-H2O"|521.3153076171875,0.126174777746201,1,"y5"|522.26531982421875,0.020523494109511,1,"KDAI+U'-H2O"|531.18572998046875,0.017260251566768,1,"a5-C1H4S1+"|592.34466552734375,0.189434334635735,1,"y6"|594.7952880859375,0.298489719629288,2,"y10+U'-H2O"|607.18060302734375,0.086959734559059,1,"b5"|651.8173828125,0.239324644207954,2,"y11+U'-H2O"|707.3721923828125,0.281166106462479,1,"y7"|717.33984375,0.240295976400375,2,"y12+U'-H2O"|735.242431640625,0.016045464202762,1,"b6"|774.85150146484375,0.075585953891277,2,"y13+U'-H2O"|781.3787841796875,0.01731531880796,1,"MQKDAI+U'-H2O"|823.3585205078125,0.348342001438141,2,"[M+2H-H2O]++ U'-H2O"|832.36456298828125,0.821685791015625,2,"[M+2H]++ U'-H2O"|842.318603515625,0.025772305205464,1,"DMNMQK+U'-H2O"|889.37774658203125,0.125654801726341,2,"[M+2H-H2O]++ U-H3PO4"|913.37347412109375,0.01973033323884,1,"MNMQKDA+U'-H2O"|929.4866943359375,0.210218042135239,1,"NMQKDAIFG-CO-C1H4S1+"|957.34912109375,0.185548722743988,1,"b7+U'-H2O"|1057.54443359375,0.119727417826653,1,"y9+U'-H2O"|1072.376708984375,0.215346395969391,1,"b8+U'-H2O"|1091.497314453125,0.02361387014389,1,"MNMQKDAIFG-CO-H3N1+"|1143.4185791015625,0.316818684339523,1,"b9+U'-H2O"|1188.582275390625,0.117498844861984,1,"y10+U'-H2O"|1189.57421875,0.046433448791504,1,"y9+U-H3PO4"|1228.488525390625,0.024275120347738,1,"a10+U'-H2O"|1256.4984130859375,0.275534242391586,1,"b10+U'-H2O"|1302.63232421875,0.042194381356239,1,"y11+U'-H2O" -36.767 933.9406 Cas7 TLALLSGKSVDEAEK U-H2O1 2 42.784267425537109 1 0.146051496267319 0,0,0,0,0,0,0,14.61,0,0,0,0,0,0,14.61 TLALLSGkSVDEAEk 1559.8407 306.0253 1865.8660 10.280866622924805 7.662559509277344 1 1 1 0 0.165740802884102 0.0 0.153031080961227 1 315.0 0 100.00 19.27 98.86 2.97 4.81 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ U'-H2O"|868.406494140625,0.043710377067328,1,"LSGKSVDE+C3O"|878.50921630859375,0.04271687194705,1,"b8+U'-H2O"|881.51123046875,0.10030597448349,1,"LALLSGK-CO+U-H3PO4"|934.4134521484375,0.175290405750275,1,"a7+U-H2O"|997.42559814453125,0.045007601380348,1,"SGKSVDEAE+U'-H2O"|1056.4964599609375,0.445992678403854,1,"y9+U'-H2O"|1143.5274658203125,0.826412320137024,1,"y10+U'-H2O"|1179.6209716796875,0.033004622906446,1,"b11+U'-H2O"|1256.603515625,0.408009380102158,1,"y11+U'-H2O"|1369.7083740234375,0.034444786608219,1,"a14-H3N1+"|1440.7257080078125,0.081928692758083,1,"b12+U-H3PO4" -37.098 735.8139 Cse1 ALYTFAEGFK U 2 76.229042053222656 1 1.608833074569702 2.46,0,0,72.55,107.41,132.71,0,158.96,160.88,0 ALYTFAEGfK 1145.5757 324.0359 1469.6116 15.1768798828125 9.470569610595703 1 1 1 0 0.253406018018723 0.0 0.216487392783165 1 315.0 0 99.17 12.14 50.50 9.25 4.24 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 112.050567626953125,0.50500750541687,1,"MI:C'"|120.080940246582031,0.095299951732159,1,"iF+"|129.102188110351563,0.130333170294762,1,"y1-H2O1+"|130.08612060546875,0.071368828415871,1,"y1-H3N1+"|136.0616455078125,0.559562504291534,1,"MI:A'"|136.075408935546875,0.991662442684174,1,"iY+"|147.112564086914063,0.158159822225571,1,"y1"|152.056777954101563,0.042359229177237,1,"MI:G'"|156.076370239257813,0.024607326835394,1,"a1+U'"|157.133209228515625,0.748135030269623,1,"a2"|185.128204345703125,0.375066697597504,1,"b2"|201.087020874023438,0.017354223877192,1,"AE"|219.112548828125,0.021971553564072,1,"YT-CO-H2O1+"|221.12786865234375,0.016703221946955,1,"TF-CO"|227.065628051757813,1.0,1,"MI:U-H3PO4"|237.122756958007813,0.131594702601433,1,"YT-CO"|240.097122192382813,0.019137103110552,1,"AEG-H2O1+"|247.106735229492188,0.082561440765858,1,"YT-H2O1+"|249.122833251953125,0.014650393277407,1,"TF"|249.15997314453125,0.018181046471,1,"LY-CO"|258.1077880859375,0.02033350430429,1,"AEG"|265.117401123046875,0.175939783453941,1,"YT"|277.154815673828125,0.013556770049036,1,"LY"|294.181427001953125,0.023879213258624,1,"y2"|302.14892578125,0.026298001408577,1,"FAE-CO-H2O1+"|320.1591796875,0.024920780211687,1,"TFA"|333.1871337890625,0.019232576712966,1,"y3-H2O1+"|348.069854736328125,0.015878442674875,1,"MI:A"|348.192169189453125,0.088175311684608,1,"b3"|351.2030029296875,0.158451542258263,1,"y3"|360.188507080078125,0.01610735617578,1,"LYT-H2O1+"|378.19952392578125,0.017009789124131,1,"LYT"|394.174468994140625,0.043824292719364,1,"YTF-H2O1+"|412.183990478515625,0.018697801977396,1,"YTF"|431.22821044921875,0.041618220508099,1,"b4-H2O1+"|449.23944091796875,0.048056524246931,1,"b4"|462.232513427734375,0.068796023726463,1,"y4-H2O1+"|463.217620849609375,0.023871500045061,1,"y4-H3N1+"|465.212799072265625,0.018635237589478,1,"YTFA-H2O1+"|480.2469482421875,0.094261720776558,1,"y4"|520.23187255859375,0.019280765205622,1,"y2+U-H3PO4"|551.2830810546875,0.251982569694519,1,"y5"|577.260986328125,0.118302121758461,1,"y3+U-H3PO4"|578.28741455078125,0.050265524536371,1,"b5-H2O1+"|594.76458740234375,0.166564807295799,2,"y8+U-H3PO4"|667.3358154296875,0.015442194417119,1,"b6"|675.23223876953125,0.025855783373117,1,"y3+U"|698.35198974609375,0.23895987868309,1,"y6"|706.304931640625,0.099407464265823,1,"y4+U-H3PO4"|736.3548583984375,0.055130917578936,1,"LYTFAEG-CO-H2O1+"|777.34149169921875,0.201728627085686,1,"y5+U-H3PO4"|799.39739990234375,0.378724426031113,1,"y7"|804.27783203125,0.018890105187893,1,"y4+U"|807.39398193359375,0.019026812165976,1,"a8-H2O1+"|810.37872314453125,0.040385793894529,1,"y6+U'"|875.3153076171875,0.051316529512405,1,"y5+U"|924.402587890625,0.237262338399887,1,"y6+U-H3PO4"|944.448486328125,0.078120112419128,1,"y8-H2O1+"|962.4586181640625,0.452546149492264,1,"y8"|1004.38104248046875,0.015123263001442,1,"y6+U-H2O"|1022.38128662109375,0.055797040462494,1,"y6+U"|1025.45751953125,0.252519190311432,1,"y7+U-H3PO4"|1043.4774169921875,0.014574917033315,1,"y7+U-HPO3"|1074.48486328125,0.046601742506027,1,"y8+U'"|1105.409912109375,0.018969278782606,1,"y7+U-H2O"|1123.4407958984375,0.078064009547234,1,"y7+U"|1128.555908203125,0.05434787273407,1,"[M+H-H2O]+"|1146.5751953125,0.472153633832932,1,"[M+H]+"|1188.5074462890625,0.148189276456833,1,"y8+U-H3PO4" -37.536 833.8672 Cse2 LVQPFGWENPR U 2 52.818855285644531 1 5.590284824371338 8.97,0,0,0,0,0,559.03,0,0,0,0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 5.432636737823486 5.498913288116455 1 1 1 0 0.222448781132698 0.0 0.252318680286407 1 315.0 0 47.85 8.60 8.42 0.00 4.17 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 112.050765991210938,0.08420105278492,1,"MI:C'"|120.080955505371094,0.248142316937447,1,"iF+"|136.061904907226563,0.478474080562592,1,"MI:A'"|152.056915283203125,0.041747037321329,1,"MI:G'"|158.092987060546875,0.02823868393898,1,"y1-H3N1+"|175.118865966796875,0.431510150432587,1,"y1"|185.164825439453125,0.975687205791473,1,"a2"|205.096786499023438,0.015142207033932,1,"FG"|208.107650756835938,0.072737187147141,1,"b1+U'-H2O"|213.159622192382813,0.55321729183197,1,"b2"|217.133560180664063,0.150055125355721,1,"PF-CO"|228.134170532226563,0.134030729532242,1,"VQ"|245.128326416015625,0.073948614299297,1,"PF"|255.145156860351563,0.044952541589737,1,"y2-H3N1+"|268.1070556640625,0.017682727426291,1,"GW-CO+C3O"|271.1207275390625,0.015898240730166,1,"FG-CO+U'-H2O"|272.17138671875,0.733417451381683,1,"y2"|302.1507568359375,0.017543597146869,1,"PFG"|323.207000732421875,0.023342134431005,1,"b3-H2O1+"|341.217620849609375,0.281899809837341,1,"b3"|368.202545166015625,0.018031865358353,1,"y3-H2O1+"|369.186676025390625,0.024854462593794,1,"y3-H3N1+"|373.18609619140625,0.037409465759993,1,"QPF"|384.165252685546875,0.020501535385847,1,"WEN-CO-H2O1+"|386.214569091796875,0.333306282758713,1,"y3"|465.113739013671875,0.085212588310242,1,"iW+U-H2O"|483.124237060546875,0.077979676425457,1,"FG-CO+U-H2O"|497.247100830078125,0.052800357341766,1,"y4-H2O1+"|515.25689697265625,0.456620991230011,1,"y4"|522.14117431640625,0.024717634543777,1,"GW-CO+U-H2O"|557.75213623046875,0.042095232754946,2,"y8+U'"|566.24700927734375,0.018172480165958,1,"GWENP-H2O1+"|612.78509521484375,0.067495785653591,2,"y9+U'-H2O"|614.77642822265625,0.18346481025219,2,"y8+U-H3PO4"|654.75494384765625,0.182821094989777,2,"y8+U-H2O"|663.76007080078125,0.391415536403656,2,"y8+U"|678.8104248046875,0.125872269272804,2,"y9+U-H3PO4"|697.19720458984375,0.01831066608429,1,"GWE+U"|718.7857666015625,0.509350657463074,2,"y9+U-H2O"|870.38726806640625,0.020341049879789,1,"y6+U'"|909.38018798828125,0.016918642446399,1,"b5+U"|941.30230712890625,0.016845868900418,1,"PFGWE+U"|984.421630859375,0.171274989843369,1,"y6+U-H3PO4"|1002.4327392578125,0.077881030738354,1,"y6+U-HPO3"|1007.3658447265625,0.02186157181859,1,"y5+U-H2O"|1017.45574951171875,0.016997389495373,1,"y7+U'"|1025.3704833984375,0.067600704729557,1,"y5+U"|1037.34326171875,0.015292263589799,1,"PFGWEN+U-H2O"|1064.37841796875,0.220285996794701,1,"y6+U-H2O"|1082.393310546875,0.415275424718857,1,"y6+U"|1114.5091552734375,0.116430044174194,1,"y8+U'"|1131.4898681640625,0.07273530960083,1,"y7+U-H3PO4"|1149.4764404296875,0.018299410119653,1,"y7+U-HPO3"|1154.4898681640625,0.135885670781136,1,"QPFGWENP-CO+U-H3PO4"|1211.4739990234375,0.09792023897171,1,"y7+U-H2O"|1228.5391845703125,0.487874060869217,1,"y8+U-H3PO4"|1246.5452880859375,0.41549888253212,1,"y8+U-HPO3"|1308.5025634765625,0.782280921936035,1,"y8+U-H2O"|1326.51611328125,1.0,1,"y8+U" -37.864 698.2974 Cas5 DEPMITLPR U 2 67.925018310546875 1 0.827892243862152 0,0,82.79,0,0,0,0,12.18,0 DEpMITLPR 1070.5430 324.0359 1394.5789 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 112.050773620605469,0.042819745838642,1,"MI:C'"|136.061843872070313,0.196844235062599,1,"MI:A'"|152.056671142578125,0.023113740608096,1,"MI:G'"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1"|182.092300415039063,0.052632980048656,1,"iP+U'"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2"|253.100723266601563,9.467311203479767e-03,1,"PM-CO+C3O"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2"|281.09564208984375,9.001040831208229e-03,1,"PM+C3O"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|313.13702392578125,0.016673086211085,1,"PM-CO+U'"|341.126983642578125,0.080299213528633,1,"PM+U'"|348.068084716796875,9.060680866241455e-03,1,"MI:A"|376.089996337890625,0.029012143611908,1,"iP+U-H2O"|385.25506591796875,0.261529922485352,1,"y3"|394.095611572265625,0.040202785283327,1,"iP+U"|426.217559814453125,7.179270498454571e-03,1,"PMI-CO+U'"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O"|454.151214599609375,0.077750355005264,1,"b3+U'"|454.217010498046875,7.962716743350029e-03,1,"PMI+U'"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4"|525.14324951171875,0.028857138007879,1,"PM-CO+U"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"PM+U-H2O"|537.2529296875,9.177219122648239e-03,1,"PMIT+U'-H2O"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|553.13372802734375,0.032937977463007,1,"PM+U"|553.27215576171875,0.012286836281419,1,"MITL+U'-H2O"|555.264404296875,9.468427859246731e-03,1,"PMIT+U'"|567.26251220703125,0.116328254342079,2,"y7+U-H2O"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U"|585.19580078125,8.00114031881094e-03,1,"b4+U'"|599.387451171875,0.483213186264038,1,"y5"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]++ U-H3PO4"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O"|649.3082275390625,0.248698011040688,2,"[M+2H]++ 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0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 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+37.864 698.2974 Cas5 DEPMITLPR U 2 67.925018310546875 1 0.827892243862152 0,0,82.79,0,0,0,0,12.18,0 DEpMITLPR 1070.5430 324.0359 1394.5789 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 112.050773620605469,0.042819745838642,1,"MI:C'+"|136.061843872070313,0.196844235062599,1,"MI:A'+"|152.056671142578125,0.023113740608096,1,"MI:G'+"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1+"|182.092300415039063,0.052632980048656,1,"iP+U'++"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2+"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2+"|253.100723266601563,9.467311203479767e-03,1,"PM-CO+C3O+"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2+"|281.09564208984375,9.001040831208229e-03,1,"PM+C3O+"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|313.13702392578125,0.016673086211085,1,"PM-CO+U'+"|341.126983642578125,0.080299213528633,1,"PM+U'+"|348.068084716796875,9.060680866241455e-03,1,"MI:A+"|376.089996337890625,0.029012143611908,1,"iP+U-H2O++"|385.25506591796875,0.261529922485352,1,"y3+"|394.095611572265625,0.040202785283327,1,"iP+U++"|426.217559814453125,7.179270498454571e-03,1,"PMI-CO+U'+"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O+"|454.151214599609375,0.077750355005264,1,"b3+U'+"|454.217010498046875,7.962716743350029e-03,1,"PMI+U'+"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4+"|525.14324951171875,0.028857138007879,1,"PM-CO+U+"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"PM+U-H2O+"|537.2529296875,9.177219122648239e-03,1,"PMIT+U'-H2O+"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|553.13372802734375,0.032937977463007,1,"PM+U+"|553.27215576171875,0.012286836281419,1,"MITL+U'-H2O+"|555.264404296875,9.468427859246731e-03,1,"PMIT+U'+"|567.26251220703125,0.116328254342079,2,"y7+U-H2O++"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U++"|585.19580078125,8.00114031881094e-03,1,"b4+U'+"|599.387451171875,0.483213186264038,1,"y5+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]+U-H3PO4++"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O+"|649.3082275390625,0.248698011040688,2,"[M+2H]+U-H3PO4++"|669.29034423828125,0.01186771504581,1,"b6-H2O1+"|699.23114013671875,0.020817343145609,1,"b4+U-H3PO4+"|730.42572021484375,0.26859325170517,1,"y6+"|749.25885009765625,8.758146315813065e-03,1,"PMIT+U-H2O+"|782.404296875,0.012716175056994,1,"EPMITLP"|784.31610107421875,7.947030477225781e-03,1,"a5+U-H3PO4+"|812.31365966796875,0.012815644964576,1,"b5+U-H3PO4+"|825.46112060546875,0.037652637809515,1,"y5+U-H3PO4+"|827.4814453125,0.037520926445723,1,"y7+"|842.45953369140625,0.042362816631794,1,"y6+U'+"|879.48016357421875,0.099386416375637,1,"y7+C3O+"|939.5068359375,0.254053741693497,1,"y8-H3N1+"|956.483642578125,0.047358602285385,1,"y6+U-H3PO4+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1071.533935546875,0.012802372686565,1,"[M+H]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4+"|1133.5010986328125,0.05346042662859,1,"y7+U-H2O+"|1151.51953125,0.053188119083643,1,"y7+U+"|1183.5704345703125,0.054004456847906,1,"[M+H]+U'+" +37.864 698.2974 DECOY_Cse1 PMVNDNILR U 2 39.625930786132813 2 0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 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129.066375732421875,0.011452200822532,1,"SS-CO-H2O1+"|136.062057495117188,0.117006808519363,1,"MI:A'+"|136.075942993164063,0.061224263161421,1,"iY+"|147.076553344726563,0.033742658793926,1,"SS-CO"|152.05645751953125,8.929258212447167e-03,1,"MI:G'+"|157.10845947265625,0.019333818927407,1,"y1-H2O1+"|158.092269897460938,0.014068718068302,1,"y1-H3N1+"|175.11895751953125,1.0,1,"y1+"|200.10223388671875,0.037957575172186,1,"AQ"|200.13934326171875,0.015138491056859,1,"NI-CO"|207.112930297851563,0.018860274925828,1,"YA-CO"|225.122817993164063,0.017288146540523,1,"SL-CO+C3O+"|227.066238403320313,0.013174916617572,1,"SS+C3O+"|228.134735107421875,0.140522807836533,1,"NI"|235.107940673828125,0.038548536598682,1,"YA"|241.081558227539063,0.010871037840843,1,"ES-CO+C3O+"|242.149642944335938,0.085332110524178,1,"SSL-CO-H2O1+"|258.1038818359375,0.021212872117758,1,"ESS-CO-H2O1+"|271.17724609375,0.036110296845436,1,"y2-H3N1+"|288.20263671875,0.540427029132843,1,"y2+"|299.1700439453125,0.077199973165989,1,"TI-CO+U'+"|301.129791259765625,0.081555679440498,1,"YA-CO+U'-H2O+"|313.187530517578125,0.047560345381498,1,"LAQ"|327.162078857421875,0.011594470590353,1,"TI+U'+"|352.200225830078125,0.011090287938714,1,"TIH"|371.19293212890625,0.051817037165165,1,"ESSL-CO-H2O1+"|373.13800048828125,0.051781021058559,1,"SS-CO+U-H3PO4+"|391.1478271484375,0.033230293542147,1,"SS-CO+U-HPO3+"|398.252685546875,0.013688288629055,1,"y3-H2O1+"|399.237579345703125,0.012889615260065,1,"y3-H3N1+"|416.261444091796875,0.611584186553955,1,"y3+"|427.2349853515625,0.017148498445749,1,"AQNI"|428.2210693359375,0.057390972971916,1,"IGESS-CO-H2O1+"|429.191436767578125,0.03929715976119,1,"YAQ-CO+U'-H2O+"|467.148712158203125,0.010170607827604,1,"IG-CO+U+"|470.27783203125,0.012210931628942,1,"y4-H3N1+"|486.22381591796875,0.018033720552921,1,"SSL-CO+U-H3PO4+"|487.298919677734375,0.575224339962006,1,"y4+"|514.23504638671875,0.032693766057491,1,"a5+"|541.30743408203125,0.047687828540802,1,"IGESSL-CO-H2O1+"|542.22161865234375,0.017067449167371,1,"b5+"|573.2657470703125,0.016528343781829,1,"YAQNI-H3N1+"|580.3065185546875,0.01648885384202,1,"IHL-CO+U-HPO3+"|596.27105712890625,0.011223017238081,1,"AQNIGE-H3N1+"|613.29095458984375,0.011800601147115,1,"GESSLR-H3N1+"|630.299072265625,0.011752335354686,1,"YAQNIG-H3N1+"|636.37835693359375,0.014756876043975,1,"TIHLAQ-CO"|647.3037109375,0.027322037145495,1,"YAQNIG"|655.31170654296875,0.017578417435288,1,"AQNIGES-CO-H3N1+"|670.329833984375,0.05509876832366,1,"LAQL+U-HPO3+"|672.33526611328125,0.207145139575005,1,"AQNIGES-CO"|725.31085205078125,0.017259709537029,1,"AQNIGE+U'+"|726.34930419921875,0.046374954283237,1,"ESSLRT+C3O+"|743.3768310546875,0.172333046793938,1,"SSLRT-CO+U-H3PO4+"|760.404296875,0.187094569206238,1,"SLRTIH+C3O+"|782.33306884765625,0.012944219633937,1,"QNIGESS-CO+U'-H2O+"|783.35302734375,0.016047228127718,1,"GESSLRT+C3O+"|819.37957763671875,0.014858706854284,1,"YYAQNI-CO+U'-H2O+"|872.4212646484375,0.172972902655602,1,"ESSLRT-CO+U-H3PO4+"|888.46136474609375,0.064613588154316,1,"NIGESSLRT-CO-C1H2N2+"|913.41937255859375,0.01632821559906,1,"QNIGESSL-CO+U'+"|967.49603271484375,0.044361278414726,1,"QNIGESSLR-H2O1+"|985.50390625,0.146545097231865,1,"QNIGESSLR"|1002.53192138671875,0.231999665498734,1,"SSLRTIHL+U'-H2O+"|1042.531005859375,0.303900748491287,1,"QNIGESSLRT-C1H2N1O1+"|1107.4403076171875,0.013903370127082,1,"QNIGESSL-CO+U-H2O+"|1125.434326171875,0.038755424320698,1,"QNIGESSL-CO+U+"|1163.456298828125,0.017250252887607,1,"GYYAQNIG-CO+U+"|1221.4688720703125,0.043008159846067,1,"b8+U+"|1413.6343994140625,0.038349222391844,1,"SSLRTIHLAQ+U-H2O+"|1414.6561279296875,0.035235911607742,1,"ESSLRTIHLA+U-H2O+" diff --git a/src/tests/topp/OpenNuXL_4_output.idXML b/src/tests/topp/OpenNuXL_4_output.idXML index f79f5dc767c..5e240a7af06 100644 --- a/src/tests/topp/OpenNuXL_4_output.idXML +++ b/src/tests/topp/OpenNuXL_4_output.idXML @@ -6,7 +6,7 @@ - + @@ -44,7 +44,7 @@ - + @@ -124,7 +124,7 @@ - + @@ -204,7 +204,7 @@ - + @@ -284,7 +284,7 @@ - + @@ -364,7 +364,7 @@ - + @@ -444,7 +444,7 @@ - + @@ -520,7 +520,7 @@ - + @@ -596,7 +596,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -748,7 +748,7 @@ - + @@ -824,7 +824,7 @@ - + @@ -904,7 +904,7 @@ - + @@ -980,7 +980,7 @@ - + @@ -1056,7 +1056,7 @@ - + @@ -1136,7 +1136,7 @@ - + @@ -1216,7 +1216,7 @@ - + @@ -1296,7 +1296,7 @@ - + @@ -1376,7 +1376,7 @@ - + @@ -1456,7 +1456,7 @@ - + @@ -1536,7 +1536,7 @@ - + @@ -1616,7 +1616,7 @@ - + @@ -1692,7 +1692,7 @@ - + @@ -1768,7 +1768,7 @@ - + @@ -1848,7 +1848,7 @@ - + @@ -1928,7 +1928,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_4_output2.tsv b/src/tests/topp/OpenNuXL_4_output2.tsv index 24a2738bc65..cafb0fec2bd 100644 --- a/src/tests/topp/OpenNuXL_4_output2.tsv +++ b/src/tests/topp/OpenNuXL_4_output2.tsv @@ -1,26 +1,26 @@ #RT m/z proteins peptide NA charge score rank best localization score localization scores best localization(s) peptide weight NA weight cross-link weight NuXL:total_loss_score NuXL:partial_loss_score CountSequenceIsTop CountSequenceCharges CountSequenceIsXL CountSequenceIsPeptide NuXL:MIC NuXL:pl_pc_MIC NuXL:pl_MIC nr_candidates -ln(poisson) isotope_error A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H fragment_annotation -17.788 712.7828 Cas7 AEADNLDDKK U-H2O1 2 69.974990844726563 1 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 306.0253 1423.5504 11.444543838500977 16.099458694458008 1 1 1 0 0.216474175453186 0.0 0.394327819347382 3 315.0 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 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306.0253 1179.5173 2.428377628326416 4.320775508880615 1 1 1 0 0.130456954240799 0.0 0.175812318921089 1 315.0 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ 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KSEQTTGISLGR U-H2O1 2 59.922630310058594 1 0.718522191047669 71.85,28.95,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 19.087356567382813 10.870758056640625 1 1 1 0 0.221869960427284 0.0 0.115903504192829 2 315.0 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 112.050689697265625,9.990843944251537e-03,1,"MI:C'"|129.102371215820313,0.013408292084932,1,"b1"|136.061798095703125,0.902763903141022,1,"MI:A'"|136.074905395507813,0.051667388528585,1,"iK(C5H10N1)C3O"|152.056564331054688,3.377486718818545e-03,1,"MI:G'"|158.092697143554688,0.024075241759419,1,"y1-H3N1+"|175.118927001953125,0.081427209079266,1,"y1"|178.097412109375,0.341100573539734,1,"iK(C5H10N1)U'-H2O"|195.123382568359375,0.017177894711494,1,"a1+U'-H2O"|215.113723754882813,0.014229998923838,1,"y2-H3N1+"|227.066909790039063,0.016493165865541,1,"MI:U-H3PO4"|232.140274047851563,0.180095225572586,1,"y2"|241.1295166015625,0.01908091455698,1,"b1+U'"|258.143798828125,3.849325468763709e-03,1,"GIS"|282.156463623046875,0.019274268299341,1,"a2+U'-H2O"|310.150787353515625,0.118582129478455,1,"b2+U'-H2O"|327.212188720703125,3.42642655596137e-03,1,"y3-H2O1+"|328.199676513671875,4.501644056290388e-03,1,"y3-H3N1+"|345.223907470703125,0.247861370444298,1,"y3"|348.0692138671875,7.973242551088333e-03,1,"MI:A"|428.180908203125,8.386147208511829e-03,1,"SEQT-H2O1+"|432.25604248046875,0.183289110660553,1,"y4"|439.19366455078125,0.044542569667101,1,"b3+U'-H2O"|490.216064453125,0.052840437740088,2,"QTTGISL-CO+U-H2O"|517.22088623046875,3.666676813736558e-03,1,"EQTTG"|529.219970703125,9.659912437200546e-03,1,"SEQTT-H2O1+"|545.3385009765625,0.023281643167138,1,"TTGISL-CO"|567.25286865234375,0.052726376801729,1,"b4+U'-H2O"|602.3612060546875,0.080439247190952,1,"TTGISLG-CO"|676.849365234375,0.461511492729187,2,"[M+2H-H2O]++ 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-33.237 510.2805 Cas7 LLKVLK U-H2O1 2 35.617866516113281 1 3.175751924514771 0,0,317.58,0,0,27.74 LLkVLK 712.5211 306.0253 1018.5464 2.676236867904663 4.84662389755249 1 1 1 0 0.182740524411201 0.0 0.375015050172806 2 315.0 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" -33.237 510.2805 DECOY_Cas7 LKLLVK U-H2O1 2 30.675045013427734 2 1.106894612312317 0,110.69,77.01,0,0,27.74 LkLLVK 712.5211 306.0253 1018.5464 2.676236867904663 4.84662389755249 1 1 1 0 0.182740524411201 0.0 0.375015050172806 2 315.0 0 1.17647397518158 4.721068859100342 0.079879306256771 0.0 0.211029142141342 2 315.0 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ 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U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"LL-CO"|227.175506591796875,0.098765894770622,1,"LL"|242.18536376953125,0.01018890645355,1,"b2"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|336.201568603515625,0.059393648058176,1,"b2+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"b4+C3O"|548.35498046875,0.371608823537827,1,"KLLV+U'-H2O"|562.3695068359375,0.036407515406609,1,"b4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" -33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 31.678943634033203 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 0.0 0.059569962322712 2 315.0 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" -34.016 790.8062 Cas7 MATSGMMTELGK U 2 73.20819091796875 1 1.918179512023926 191.82,126.75,97.82,0,0,37.65,37.65,0,0,0,0,0 mATSGMMTELGK 1255.5611 324.0359 1579.5969 19.278144836425781 11.713431358337402 1 1 1 0 0.371337056159973 0.0 0.24375793337822 1 315.0 0 5.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.0004 0.5 1580.6042 790.8057 527.5396 395.9065 127.086746215820313,0.03221358731389,1,"a2-C1H4S1+"|129.102340698242188,0.159227415919304,1,"y1-H2O1+"|130.086349487304688,0.051548503339291,1,"y1-H3N1+"|136.061599731445313,0.055803153663874,1,"MI:A'"|147.1126708984375,0.148163199424744,1,"y1"|155.081497192382813,0.034486405551434,1,"b2-C1H4S1+"|161.09222412109375,0.014802157878876,1,"TS-CO"|171.076675415039063,0.03485019877553,1,"TS-H2O1+"|173.092819213867188,0.028763445094228,1,"AT"|175.087371826171875,0.010726612992585,1,"a2"|186.123825073242188,0.109146893024445,1,"y2-H2O1+"|187.108383178710938,0.012273258529603,1,"y2-H3N1+"|189.0869140625,0.018883759155869,1,"TS"|204.134185791015625,0.664878964424133,1,"y2"|215.083221435546875,0.011490193195641,1,"MM-C1H4S1+"|216.079666137695313,0.14799277484417,1,"a1+U'"|228.098098754882813,0.016218513250351,1,"SGM-C1H4S1+"|228.134857177734375,0.010106886737049,1,"a3-C1H4S1+"|231.098358154296875,0.02963631041348,1,"TE"|233.09527587890625,0.010079103522003,1,"MT"|241.0823974609375,0.03026669844985,1,"TS+C3O"|256.129425048828125,0.036421522498131,1,"b3-C1H4S1+"|275.06927490234375,0.321486562490463,1,"iM+U-H3PO4"|287.116729736328125,0.106576167047024,1,"a2+U'"|315.11212158203125,0.182710662484169,1,"b2+U'"|317.21807861328125,0.5060915350914,1,"y3"|330.111419677734375,0.107610121369362,1,"a1+U-H3PO4"|344.18218994140625,0.014792915433645,1,"TEL"|362.13836669921875,0.03236985206604,1,"MTE"|373.04638671875,0.055028561502695,1,"iM+U"|398.15032958984375,0.053473096340895,1,"b3+U'-H2O"|401.148590087890625,0.368163228034973,1,"TSGM-CO+C3O"|401.2054443359375,0.016921009868383,1,"TELG"|416.1590576171875,0.204516366124153,1,"b3+U'"|421.157745361328125,0.010915133170784,1,"GMMT"|428.089111328125,0.018594333902001,1,"a1+U"|428.249847412109375,0.052017502486706,1,"y4-H2O1+"|429.14337158203125,0.84875214099884,1,"TSGM+C3O"|446.26116943359375,0.214159980416298,1,"y4"|475.222991943359375,0.012469680979848,1,"MTEL"|485.180511474609375,0.03207815811038,1,"b4+U'-H2O"|490.177520751953125,0.032220557332039,1,"TSGMM-H2O1+"|508.19189453125,0.012716436758637,1,"TSGMM"|529.29425048828125,0.015442945063114,1,"y5-H2O1+"|530.19122314453125,0.180141240358353,1,"b3+U-H3PO4"|532.1845703125,0.013560008257627,1,"GMMTE-H2O1+"|542.2000732421875,0.010952124372125,1,"b5+U'-H2O"|547.30767822265625,0.328858405351639,1,"y5"|550.20074462890625,0.012767584063113,1,"GMMTE"|587.2828369140625,0.01402248814702,1,"GMMTEL-CO-C1H4S1+"|589.23138427734375,0.013000959530473,1,"SGMMTE-C1H4S1+"|604.78570556640625,0.331091970205307,2,"[M+2H]-CH4S"|619.224365234375,0.037525855004787,1,"SGMMTE-H2O1+"|631.2183837890625,0.011294193565845,1,"b6+C3O"|637.2349853515625,0.038924634456635,1,"SGMMTE"|645.2703857421875,0.017423829063773,1,"GMMTEL-H2O1+"|663.287109375,0.01368575822562,1,"GMMTEL"|673.23809814453125,0.050370126962662,1,"b6+U'-H2O"|675.79296875,0.031400952488184,2,"[M+2H]++ U'-H2O"|678.34820556640625,0.334554493427277,1,"y6"|720.27740478515625,0.039541512727737,1,"TSGMMTE-H2O1+"|732.30474853515625,0.01200485881418,1,"SGMMTEL-H2O1+"|732.81005859375,0.290660262107849,2,"[M+2H-H2O]++ U-H3PO4"|738.28192138671875,0.013668600469828,1,"TSGMMTE"|741.81646728515625,1.0,2,"[M+2H]++ U-H3PO4"|750.3192138671875,0.014047367498279,1,"SGMMTEL"|777.29205322265625,0.015259876847267,1,"a6+U-H3PO4"|805.287353515625,0.180637359619141,1,"b6+U-H3PO4"|809.39007568359375,0.169192254543304,1,"y7"|833.35845947265625,0.018561428412795,1,"TSGMMTEL-H2O1+"|851.35504150390625,0.011303779669106,1,"TSGMMTEL"|866.41046142578125,0.621590375900269,1,"y8"|935.43035888671875,0.04818819090724,1,"y9-H2O1+"|936.31427001953125,0.07395213842392,1,"b7+U-H3PO4"|953.44305419921875,0.880237638950348,1,"y9"|1036.4752197265625,0.154976740479469,1,"y10-H2O1+"|1037.4661865234375,0.044277537614107,1,"y10-H3N1+"|1054.489013671875,0.891642868518829,1,"y10"|1107.508056640625,0.010800593532622,1,"y11-H2O1+"|1125.5260009765625,0.135128006339073,1,"y11"|1166.414794921875,0.100423000752926,1,"b9+U-H3PO4"|1279.4962158203125,0.065082639455795,1,"b10+U-H3PO4"|1308.5689697265625,0.035434119403362,1,"[M+H]+ C3O" -34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U 2 37.691276550292969 1 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 324.0359 1294.4975 6.533727645874023 1.259999871253967 1 1 1 0 0.223560705780983 0.0 0.098648108541965 2 315.0 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U" -36.528 938.3693 Cas7 DDMNMQKDAIFGGK U-H2O1 2 45.990291595458984 1 1.136792063713074 0,0,0,0,0,0,113.68,0,0,0,0,0,0,11.93 DDMNMQkDAIFGGK 1568.6963 306.0253 1874.7216 14.737911224365234 7.284058094024658 1 1 1 0 0.299404740333557 0.0 0.158554673194885 1 315.0 0 60.88 11.73 11.30 0.00 6.83 0.00 0.00 0.00 -0.0012 1.2 1875.7289 938.3681 625.9145 469.6877 112.050605773925781,0.113011009991169,1,"MI:C'"|120.08087158203125,0.052033305168152,1,"iF+"|129.10211181640625,0.21279302239418,1,"y1-H2O1+"|130.086380004882813,0.07728461176157,1,"y1-H3N1+"|136.061721801757813,0.608757317066193,1,"MI:A'"|147.112777709960938,0.152066215872765,1,"y1"|152.056549072265625,0.068255327641964,1,"MI:G'"|178.096817016601563,0.119268953800201,1,"iK(C5H10N1)U'-H2O"|186.123748779296875,0.069755658507347,1,"y2-H2O1+"|204.133987426757813,0.293571650981903,1,"y2"|227.06640625,0.015322148799896,1,"MI:U-H3PO4"|231.061355590820313,0.064788468182087,1,"b2"|243.144866943359375,0.019257104024291,1,"y3-H2O1+"|246.090835571289063,0.09425338357687,1,"MN"|261.1553955078125,0.74517822265625,1,"y3"|338.144195556640625,0.02742194198072,1,"KD+U'-H2O"|344.14312744140625,0.023650586605072,1,"MQ-CO+U'"|348.07073974609375,0.025085339322686,1,"MI:A"|362.098541259765625,0.09182520955801,1,"b3"|408.223114013671875,1.0,1,"y4"|431.12469482421875,0.016397748142481,1,"a4-H3N1+"|476.143310546875,0.111722677946091,1,"b4"|494.268829345703125,0.014951772987843,1,"KDAI-CO+U'-H2O"|521.3153076171875,0.126174777746201,1,"y5"|522.26531982421875,0.020523494109511,1,"KDAI+U'-H2O"|531.18572998046875,0.017260251566768,1,"a5-C1H4S1+"|592.34466552734375,0.189434334635735,1,"y6"|594.7952880859375,0.298489719629288,2,"y10+U'-H2O"|607.18060302734375,0.086959734559059,1,"b5"|651.8173828125,0.239324644207954,2,"y11+U'-H2O"|707.3721923828125,0.281166106462479,1,"y7"|717.33984375,0.240295976400375,2,"y12+U'-H2O"|735.242431640625,0.016045464202762,1,"b6"|774.85150146484375,0.075585953891277,2,"y13+U'-H2O"|781.3787841796875,0.01731531880796,1,"MQKDAI+U'-H2O"|823.3585205078125,0.348342001438141,2,"[M+2H-H2O]++ U'-H2O"|832.36456298828125,0.821685791015625,2,"[M+2H]++ U'-H2O"|842.318603515625,0.025772305205464,1,"DMNMQK+U'-H2O"|889.37774658203125,0.125654801726341,2,"[M+2H-H2O]++ U-H3PO4"|913.37347412109375,0.01973033323884,1,"MNMQKDA+U'-H2O"|929.4866943359375,0.210218042135239,1,"NMQKDAIFG-CO-C1H4S1+"|957.34912109375,0.185548722743988,1,"b7+U'-H2O"|1057.54443359375,0.119727417826653,1,"y9+U'-H2O"|1072.376708984375,0.215346395969391,1,"b8+U'-H2O"|1091.497314453125,0.02361387014389,1,"MNMQKDAIFG-CO-H3N1+"|1143.4185791015625,0.316818684339523,1,"b9+U'-H2O"|1188.582275390625,0.117498844861984,1,"y10+U'-H2O"|1189.57421875,0.046433448791504,1,"y9+U-H3PO4"|1228.488525390625,0.024275120347738,1,"a10+U'-H2O"|1256.4984130859375,0.275534242391586,1,"b10+U'-H2O"|1302.63232421875,0.042194381356239,1,"y11+U'-H2O" -36.767 933.9406 Cas7 TLALLSGKSVDEAEK U-H2O1 2 42.784267425537109 1 0.146051496267319 0,0,0,0,0,0,0,14.61,0,0,0,0,0,0,14.61 TLALLSGkSVDEAEk 1559.8407 306.0253 1865.8660 10.280866622924805 7.662559509277344 1 1 1 0 0.165740802884102 0.0 0.153031080961227 1 315.0 0 100.00 19.27 98.86 2.97 4.81 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ U'-H2O"|868.406494140625,0.043710377067328,1,"LSGKSVDE+C3O"|878.50921630859375,0.04271687194705,1,"b8+U'-H2O"|881.51123046875,0.10030597448349,1,"LALLSGK-CO+U-H3PO4"|934.4134521484375,0.175290405750275,1,"a7+U-H2O"|997.42559814453125,0.045007601380348,1,"SGKSVDEAE+U'-H2O"|1056.4964599609375,0.445992678403854,1,"y9+U'-H2O"|1143.5274658203125,0.826412320137024,1,"y10+U'-H2O"|1179.6209716796875,0.033004622906446,1,"b11+U'-H2O"|1256.603515625,0.408009380102158,1,"y11+U'-H2O"|1369.7083740234375,0.034444786608219,1,"a14-H3N1+"|1440.7257080078125,0.081928692758083,1,"b12+U-H3PO4" -37.098 735.8139 Cse1 ALYTFAEGFK U 2 76.229042053222656 1 1.608833074569702 2.46,0,0,72.55,107.41,132.71,0,158.96,160.88,0 ALYTFAEGfK 1145.5757 324.0359 1469.6116 15.1768798828125 9.470569610595703 1 1 1 0 0.253406018018723 0.0 0.216487392783165 1 315.0 0 99.17 12.14 50.50 9.25 4.24 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 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-37.536 833.8672 Cse2 LVQPFGWENPR U 2 52.818855285644531 1 5.590284824371338 8.97,0,0,0,0,0,559.03,0,0,0,0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 5.432636737823486 5.498913288116455 1 1 1 0 0.222448781132698 0.0 0.252318680286407 1 315.0 0 47.85 8.60 8.42 0.00 4.17 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 112.050765991210938,0.08420105278492,1,"MI:C'"|120.080955505371094,0.248142316937447,1,"iF+"|136.061904907226563,0.478474080562592,1,"MI:A'"|152.056915283203125,0.041747037321329,1,"MI:G'"|158.092987060546875,0.02823868393898,1,"y1-H3N1+"|175.118865966796875,0.431510150432587,1,"y1"|185.164825439453125,0.975687205791473,1,"a2"|205.096786499023438,0.015142207033932,1,"FG"|208.107650756835938,0.072737187147141,1,"b1+U'-H2O"|213.159622192382813,0.55321729183197,1,"b2"|217.133560180664063,0.150055125355721,1,"PF-CO"|228.134170532226563,0.134030729532242,1,"VQ"|245.128326416015625,0.073948614299297,1,"PF"|255.145156860351563,0.044952541589737,1,"y2-H3N1+"|268.1070556640625,0.017682727426291,1,"GW-CO+C3O"|271.1207275390625,0.015898240730166,1,"FG-CO+U'-H2O"|272.17138671875,0.733417451381683,1,"y2"|302.1507568359375,0.017543597146869,1,"PFG"|323.207000732421875,0.023342134431005,1,"b3-H2O1+"|341.217620849609375,0.281899809837341,1,"b3"|368.202545166015625,0.018031865358353,1,"y3-H2O1+"|369.186676025390625,0.024854462593794,1,"y3-H3N1+"|373.18609619140625,0.037409465759993,1,"QPF"|384.165252685546875,0.020501535385847,1,"WEN-CO-H2O1+"|386.214569091796875,0.333306282758713,1,"y3"|465.113739013671875,0.085212588310242,1,"iW+U-H2O"|483.124237060546875,0.077979676425457,1,"FG-CO+U-H2O"|497.247100830078125,0.052800357341766,1,"y4-H2O1+"|515.25689697265625,0.456620991230011,1,"y4"|522.14117431640625,0.024717634543777,1,"GW-CO+U-H2O"|557.75213623046875,0.042095232754946,2,"y8+U'"|566.24700927734375,0.018172480165958,1,"GWENP-H2O1+"|612.78509521484375,0.067495785653591,2,"y9+U'-H2O"|614.77642822265625,0.18346481025219,2,"y8+U-H3PO4"|654.75494384765625,0.182821094989777,2,"y8+U-H2O"|663.76007080078125,0.391415536403656,2,"y8+U"|678.8104248046875,0.125872269272804,2,"y9+U-H3PO4"|697.19720458984375,0.01831066608429,1,"GWE+U"|718.7857666015625,0.509350657463074,2,"y9+U-H2O"|870.38726806640625,0.020341049879789,1,"y6+U'"|909.38018798828125,0.016918642446399,1,"b5+U"|941.30230712890625,0.016845868900418,1,"PFGWE+U"|984.421630859375,0.171274989843369,1,"y6+U-H3PO4"|1002.4327392578125,0.077881030738354,1,"y6+U-HPO3"|1007.3658447265625,0.02186157181859,1,"y5+U-H2O"|1017.45574951171875,0.016997389495373,1,"y7+U'"|1025.3704833984375,0.067600704729557,1,"y5+U"|1037.34326171875,0.015292263589799,1,"PFGWEN+U-H2O"|1064.37841796875,0.220285996794701,1,"y6+U-H2O"|1082.393310546875,0.415275424718857,1,"y6+U"|1114.5091552734375,0.116430044174194,1,"y8+U'"|1131.4898681640625,0.07273530960083,1,"y7+U-H3PO4"|1149.4764404296875,0.018299410119653,1,"y7+U-HPO3"|1154.4898681640625,0.135885670781136,1,"QPFGWENP-CO+U-H3PO4"|1211.4739990234375,0.09792023897171,1,"y7+U-H2O"|1228.5391845703125,0.487874060869217,1,"y8+U-H3PO4"|1246.5452880859375,0.41549888253212,1,"y8+U-HPO3"|1308.5025634765625,0.782280921936035,1,"y8+U-H2O"|1326.51611328125,1.0,1,"y8+U" -37.864 698.2974 Cas5 DEPMITLPR U 2 67.925018310546875 1 0.827892243862152 0,0,82.79,0,0,0,0,12.18,0 DEpMITLPR 1070.5430 324.0359 1394.5789 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 112.050773620605469,0.042819745838642,1,"MI:C'"|136.061843872070313,0.196844235062599,1,"MI:A'"|152.056671142578125,0.023113740608096,1,"MI:G'"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1"|182.092300415039063,0.052632980048656,1,"iP+U'"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2"|253.100723266601563,9.467311203479767e-03,1,"PM-CO+C3O"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2"|281.09564208984375,9.001040831208229e-03,1,"PM+C3O"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|313.13702392578125,0.016673086211085,1,"PM-CO+U'"|341.126983642578125,0.080299213528633,1,"PM+U'"|348.068084716796875,9.060680866241455e-03,1,"MI:A"|376.089996337890625,0.029012143611908,1,"iP+U-H2O"|385.25506591796875,0.261529922485352,1,"y3"|394.095611572265625,0.040202785283327,1,"iP+U"|426.217559814453125,7.179270498454571e-03,1,"PMI-CO+U'"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O"|454.151214599609375,0.077750355005264,1,"b3+U'"|454.217010498046875,7.962716743350029e-03,1,"PMI+U'"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4"|525.14324951171875,0.028857138007879,1,"PM-CO+U"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"PM+U-H2O"|537.2529296875,9.177219122648239e-03,1,"PMIT+U'-H2O"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|553.13372802734375,0.032937977463007,1,"PM+U"|553.27215576171875,0.012286836281419,1,"MITL+U'-H2O"|555.264404296875,9.468427859246731e-03,1,"PMIT+U'"|567.26251220703125,0.116328254342079,2,"y7+U-H2O"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U"|585.19580078125,8.00114031881094e-03,1,"b4+U'"|599.387451171875,0.483213186264038,1,"y5"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]++ U-H3PO4"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O"|649.3082275390625,0.248698011040688,2,"[M+2H]++ 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0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 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+37.864 698.2974 Cas5 DEPMITLPR U 2 67.925018310546875 1 0.827892243862152 0,0,82.79,0,0,0,0,12.18,0 DEpMITLPR 1070.5430 324.0359 1394.5789 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 112.050773620605469,0.042819745838642,1,"MI:C'+"|136.061843872070313,0.196844235062599,1,"MI:A'+"|152.056671142578125,0.023113740608096,1,"MI:G'+"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1+"|182.092300415039063,0.052632980048656,1,"iP+U'++"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2+"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2+"|253.100723266601563,9.467311203479767e-03,1,"PM-CO+C3O+"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2+"|281.09564208984375,9.001040831208229e-03,1,"PM+C3O+"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|313.13702392578125,0.016673086211085,1,"PM-CO+U'+"|341.126983642578125,0.080299213528633,1,"PM+U'+"|348.068084716796875,9.060680866241455e-03,1,"MI:A+"|376.089996337890625,0.029012143611908,1,"iP+U-H2O++"|385.25506591796875,0.261529922485352,1,"y3+"|394.095611572265625,0.040202785283327,1,"iP+U++"|426.217559814453125,7.179270498454571e-03,1,"PMI-CO+U'+"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O+"|454.151214599609375,0.077750355005264,1,"b3+U'+"|454.217010498046875,7.962716743350029e-03,1,"PMI+U'+"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4+"|525.14324951171875,0.028857138007879,1,"PM-CO+U+"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"PM+U-H2O+"|537.2529296875,9.177219122648239e-03,1,"PMIT+U'-H2O+"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|553.13372802734375,0.032937977463007,1,"PM+U+"|553.27215576171875,0.012286836281419,1,"MITL+U'-H2O+"|555.264404296875,9.468427859246731e-03,1,"PMIT+U'+"|567.26251220703125,0.116328254342079,2,"y7+U-H2O++"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U++"|585.19580078125,8.00114031881094e-03,1,"b4+U'+"|599.387451171875,0.483213186264038,1,"y5+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]+U-H3PO4++"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O+"|649.3082275390625,0.248698011040688,2,"[M+2H]+U-H3PO4++"|669.29034423828125,0.01186771504581,1,"b6-H2O1+"|699.23114013671875,0.020817343145609,1,"b4+U-H3PO4+"|730.42572021484375,0.26859325170517,1,"y6+"|749.25885009765625,8.758146315813065e-03,1,"PMIT+U-H2O+"|782.404296875,0.012716175056994,1,"EPMITLP"|784.31610107421875,7.947030477225781e-03,1,"a5+U-H3PO4+"|812.31365966796875,0.012815644964576,1,"b5+U-H3PO4+"|825.46112060546875,0.037652637809515,1,"y5+U-H3PO4+"|827.4814453125,0.037520926445723,1,"y7+"|842.45953369140625,0.042362816631794,1,"y6+U'+"|879.48016357421875,0.099386416375637,1,"y7+C3O+"|939.5068359375,0.254053741693497,1,"y8-H3N1+"|956.483642578125,0.047358602285385,1,"y6+U-H3PO4+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1071.533935546875,0.012802372686565,1,"[M+H]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4+"|1133.5010986328125,0.05346042662859,1,"y7+U-H2O+"|1151.51953125,0.053188119083643,1,"y7+U+"|1183.5704345703125,0.054004456847906,1,"[M+H]+U'+" +37.864 698.2974 DECOY_Cse1 PMVNDNILR U 2 39.625930786132813 2 0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 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+40.038 1043.4525 Cas7 SGYYAQNIGESSLRTIHLAQLR GU-H2O1 3 12.18718147277832 1 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 4.506982803344727 0.042108997702599 1 1 1 0 0.193572551012039 0.0 2.997914329171181e-03 1 315.0 0 11.70 1.76 0.00 0.00 0.89 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 129.066375732421875,0.011452200822532,1,"SS-CO-H2O1+"|136.062057495117188,0.117006808519363,1,"MI:A'+"|136.075942993164063,0.061224263161421,1,"iY+"|147.076553344726563,0.033742658793926,1,"SS-CO"|152.05645751953125,8.929258212447167e-03,1,"MI:G'+"|157.10845947265625,0.019333818927407,1,"y1-H2O1+"|158.092269897460938,0.014068718068302,1,"y1-H3N1+"|175.11895751953125,1.0,1,"y1+"|200.10223388671875,0.037957575172186,1,"AQ"|200.13934326171875,0.015138491056859,1,"NI-CO"|207.112930297851563,0.018860274925828,1,"YA-CO"|225.122817993164063,0.017288146540523,1,"SL-CO+C3O+"|227.066238403320313,0.013174916617572,1,"SS+C3O+"|228.134735107421875,0.140522807836533,1,"NI"|235.107940673828125,0.038548536598682,1,"YA"|241.081558227539063,0.010871037840843,1,"ES-CO+C3O+"|242.149642944335938,0.085332110524178,1,"SSL-CO-H2O1+"|258.1038818359375,0.021212872117758,1,"ESS-CO-H2O1+"|271.17724609375,0.036110296845436,1,"y2-H3N1+"|288.20263671875,0.540427029132843,1,"y2+"|299.1700439453125,0.077199973165989,1,"TI-CO+U'+"|301.129791259765625,0.081555679440498,1,"YA-CO+U'-H2O+"|313.187530517578125,0.047560345381498,1,"LAQ"|327.162078857421875,0.011594470590353,1,"TI+U'+"|352.200225830078125,0.011090287938714,1,"TIH"|371.19293212890625,0.051817037165165,1,"ESSL-CO-H2O1+"|373.13800048828125,0.051781021058559,1,"SS-CO+U-H3PO4+"|391.1478271484375,0.033230293542147,1,"SS-CO+U-HPO3+"|398.252685546875,0.013688288629055,1,"y3-H2O1+"|399.237579345703125,0.012889615260065,1,"y3-H3N1+"|416.261444091796875,0.611584186553955,1,"y3+"|427.2349853515625,0.017148498445749,1,"AQNI"|428.2210693359375,0.057390972971916,1,"IGESS-CO-H2O1+"|429.191436767578125,0.03929715976119,1,"YAQ-CO+U'-H2O+"|467.148712158203125,0.010170607827604,1,"IG-CO+U+"|470.27783203125,0.012210931628942,1,"y4-H3N1+"|486.22381591796875,0.018033720552921,1,"SSL-CO+U-H3PO4+"|487.298919677734375,0.575224339962006,1,"y4+"|514.23504638671875,0.032693766057491,1,"a5+"|541.30743408203125,0.047687828540802,1,"IGESSL-CO-H2O1+"|542.22161865234375,0.017067449167371,1,"b5+"|573.2657470703125,0.016528343781829,1,"YAQNI-H3N1+"|580.3065185546875,0.01648885384202,1,"IHL-CO+U-HPO3+"|596.27105712890625,0.011223017238081,1,"AQNIGE-H3N1+"|613.29095458984375,0.011800601147115,1,"GESSLR-H3N1+"|630.299072265625,0.011752335354686,1,"YAQNIG-H3N1+"|636.37835693359375,0.014756876043975,1,"TIHLAQ-CO"|647.3037109375,0.027322037145495,1,"YAQNIG"|655.31170654296875,0.017578417435288,1,"AQNIGES-CO-H3N1+"|670.329833984375,0.05509876832366,1,"LAQL+U-HPO3+"|672.33526611328125,0.207145139575005,1,"AQNIGES-CO"|725.31085205078125,0.017259709537029,1,"AQNIGE+U'+"|726.34930419921875,0.046374954283237,1,"ESSLRT+C3O+"|743.3768310546875,0.172333046793938,1,"SSLRT-CO+U-H3PO4+"|760.404296875,0.187094569206238,1,"SLRTIH+C3O+"|782.33306884765625,0.012944219633937,1,"QNIGESS-CO+U'-H2O+"|783.35302734375,0.016047228127718,1,"GESSLRT+C3O+"|819.37957763671875,0.014858706854284,1,"YYAQNI-CO+U'-H2O+"|872.4212646484375,0.172972902655602,1,"ESSLRT-CO+U-H3PO4+"|888.46136474609375,0.064613588154316,1,"NIGESSLRT-CO-C1H2N2+"|913.41937255859375,0.01632821559906,1,"QNIGESSL-CO+U'+"|967.49603271484375,0.044361278414726,1,"QNIGESSLR-H2O1+"|985.50390625,0.146545097231865,1,"QNIGESSLR"|1002.53192138671875,0.231999665498734,1,"SSLRTIHL+U'-H2O+"|1042.531005859375,0.303900748491287,1,"QNIGESSLRT-C1H2N1O1+"|1107.4403076171875,0.013903370127082,1,"QNIGESSL-CO+U-H2O+"|1125.434326171875,0.038755424320698,1,"QNIGESSL-CO+U+"|1163.456298828125,0.017250252887607,1,"GYYAQNIG-CO+U+"|1221.4688720703125,0.043008159846067,1,"b8+U+"|1413.6343994140625,0.038349222391844,1,"SSLRTIHLAQ+U-H2O+"|1414.6561279296875,0.035235911607742,1,"ESSLRTIHLA+U-H2O+" diff --git a/src/tests/topp/OpenNuXL_5_output.idXML b/src/tests/topp/OpenNuXL_5_output.idXML index c46c4219bf7..734ec280a85 100644 --- a/src/tests/topp/OpenNuXL_5_output.idXML +++ b/src/tests/topp/OpenNuXL_5_output.idXML @@ -6,7 +6,7 @@ - + @@ -32,7 +32,7 @@ - + @@ -112,7 +112,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -272,7 +272,7 @@ - + @@ -352,7 +352,7 @@ - + @@ -432,7 +432,7 @@ - + @@ -512,7 +512,7 @@ - + @@ -592,7 +592,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -752,7 +752,7 @@ - + @@ -832,7 +832,7 @@ - + @@ -912,7 +912,7 @@ - + @@ -992,7 +992,7 @@ - + @@ -1072,7 +1072,7 @@ - + @@ -1152,7 +1152,7 @@ - + @@ -1232,7 +1232,7 @@ - + @@ -1312,7 +1312,7 @@ - + @@ -1392,7 +1392,7 @@ - + @@ -1472,7 +1472,7 @@ - + @@ -1552,7 +1552,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_6_output.idXML b/src/tests/topp/OpenNuXL_6_output.idXML index cb76bda8321..fdbbb456e79 100644 --- a/src/tests/topp/OpenNuXL_6_output.idXML +++ b/src/tests/topp/OpenNuXL_6_output.idXML @@ -6,7 +6,7 @@ - + @@ -36,7 +36,7 @@ - + @@ -112,7 +112,7 @@ - + @@ -188,7 +188,7 @@ - + @@ -260,7 +260,7 @@ - + @@ -340,7 +340,7 @@ - + @@ -416,7 +416,7 @@ - + @@ -492,7 +492,7 @@ - + @@ -568,7 +568,7 @@ - + @@ -644,7 +644,7 @@ - + @@ -720,7 +720,7 @@ - + @@ -796,7 +796,7 @@ - + @@ -872,7 +872,7 @@ - + @@ -948,7 +948,7 @@ - + @@ -1024,7 +1024,7 @@ - + @@ -1100,7 +1100,7 @@ - + @@ -1176,7 +1176,7 @@ - + @@ -1252,7 +1252,7 @@ - + @@ -1328,7 +1328,7 @@ - + @@ -1404,7 +1404,7 @@ - + @@ -1480,7 +1480,7 @@ - + @@ -1556,7 +1556,7 @@ - + @@ -1632,7 +1632,7 @@ - + @@ -1708,7 +1708,7 @@ - + @@ -1788,7 +1788,7 @@ - + @@ -1864,7 +1864,7 @@ - + @@ -1940,7 +1940,7 @@ - + @@ -2012,7 +2012,7 @@ - + @@ -2088,7 +2088,7 @@ - + @@ -2164,7 +2164,7 @@ - + @@ -2240,7 +2240,7 @@ - + @@ -2316,7 +2316,7 @@ - + @@ -2392,7 +2392,7 @@ - + @@ -2468,7 +2468,7 @@ - + @@ -2544,7 +2544,7 @@ - + @@ -2620,7 +2620,7 @@ - + @@ -2696,7 +2696,7 @@ - + @@ -2772,7 +2772,7 @@ - + @@ -2848,7 +2848,7 @@ - + @@ -2928,7 +2928,7 @@ - + @@ -3004,7 +3004,7 @@ - + @@ -3080,7 +3080,7 @@ - + @@ -3156,7 +3156,7 @@ - + @@ -3236,7 +3236,7 @@ - + @@ -3312,7 +3312,7 @@ - + @@ -3388,7 +3388,7 @@ - + @@ -3464,7 +3464,7 @@ - + @@ -3540,7 +3540,7 @@ - + @@ -3616,7 +3616,7 @@ - + @@ -3692,7 +3692,7 @@ - + @@ -3768,7 +3768,7 @@ - + @@ -3848,7 +3848,7 @@ - + @@ -3924,7 +3924,7 @@ - + @@ -4000,7 +4000,7 @@ - + @@ -4076,7 +4076,7 @@ - + @@ -4156,7 +4156,7 @@ - + @@ -4232,7 +4232,7 @@ - + @@ -4308,7 +4308,7 @@ - + @@ -4384,7 +4384,7 @@ - + @@ -4460,7 +4460,7 @@ - + @@ -4536,7 +4536,7 @@ - + @@ -4612,7 +4612,7 @@ - + @@ -4688,7 +4688,7 @@ - + @@ -4764,7 +4764,7 @@ - + @@ -4840,7 +4840,7 @@ - + @@ -4916,7 +4916,7 @@ - + @@ -4992,7 +4992,7 @@ - + @@ -5068,7 +5068,7 @@ - + @@ -5144,7 +5144,7 @@ - + @@ -5220,7 +5220,7 @@ - + @@ -5292,7 +5292,7 @@ - + @@ -5372,7 +5372,7 @@ - + @@ -5448,7 +5448,7 @@ - + @@ -5524,7 +5524,7 @@ - + @@ -5600,7 +5600,7 @@ - + @@ -5680,7 +5680,7 @@ - + @@ -5756,7 +5756,7 @@ - + @@ -5832,7 +5832,7 @@ - + @@ -5908,7 +5908,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_6_output2.tsv b/src/tests/topp/OpenNuXL_6_output2.tsv index 893eeb91876..25cec195212 100644 --- a/src/tests/topp/OpenNuXL_6_output2.tsv +++ b/src/tests/topp/OpenNuXL_6_output2.tsv @@ -1,81 +1,81 @@ #RT m/z proteins peptide NA charge score rank best localization score localization scores best localization(s) peptide weight NA weight cross-link weight NuXL:total_loss_score NuXL:partial_loss_score CountSequenceIsTop CountSequenceCharges CountSequenceIsXL CountSequenceIsPeptide NuXL:MIC NuXL:pl_pc_MIC NuXL:pl_MIC nr_candidates -ln(poisson) isotope_error A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H fragment_annotation -17.788 712.7828 Cas7 AEADNLDDKK U-H3O4P1 2 66.026290893554688 1 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 226.0590 1343.5841 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 55.851314362896943 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -39.9835 59428.6 1344.5914 672.7993 448.8686 336.9033 112.050621032714844,0.028104400262237,1,"MI:C'"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O"|501.19091796875,0.035030111670494,1,"b5"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O"|584.267578125,9.894491173326969e-03,1,"LDDK+U'"|586.28167724609375,0.011093857698143,1,"a6"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]++ U'-H2O"|599.27777099609375,0.764611601829529,1,"y4+U'-H2O"|606.77734375,0.299497008323669,2,"[M+2H]++ U'-H2O"|614.27984619140625,0.039939478039742,1,"b6"|680.2978515625,0.018134105950594,1,"a6+U'-H2O"|698.31036376953125,6.59028347581625e-03,1,"LDDK+U-H3PO4"|712.36236572265625,0.394213527441025,1,"y5+U'-H2O"|729.31292724609375,6.610926240682602e-03,1,"b7"|795.32373046875,0.023242574185133,1,"a7+U'-H2O"|826.40509033203125,0.400069534778595,1,"y6+U'-H2O"|844.32489013671875,6.451499182730913e-03,1,"b8"|866.3614501953125,0.062791705131531,1,"ADNLDDK+U'-H2O"|884.37408447265625,7.893706671893597e-03,1,"EADNLDDK-H3N1+"|941.43206787109375,0.44364058971405,1,"y7+U'-H2O"|1012.468994140625,0.708723366260529,1,"y8+U'-H2O"|1066.4478759765625,0.035385373979807,1,"b9+U'-H2O"|1141.5120849609375,7.319674827158451e-03,1,"y9+U'-H2O"|1212.5546875,0.066727869212627,1,"[M+H]+ U'-H2O" -17.788 712.7828 Cas7 AEADNLDDKK U-H2O1 2 65.480873107910156 2 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 306.0253 1423.5504 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 55.851314362896943 0 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 55.851314362896943 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 112.050621032714844,0.028104400262237,1,"MI:C'"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O"|501.19091796875,0.035030111670494,1,"b5"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O"|584.267578125,9.894491173326969e-03,1,"LDDK+U'"|586.28167724609375,0.011093857698143,1,"a6"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]++ U'-H2O"|599.27777099609375,0.764611601829529,1,"y4+U'-H2O"|606.77734375,0.299497008323669,2,"[M+2H]++ U'-H2O"|614.27984619140625,0.039939478039742,1,"b6"|680.2978515625,0.018134105950594,1,"a6+U'-H2O"|698.31036376953125,6.59028347581625e-03,1,"LDDK+U-H3PO4"|712.36236572265625,0.394213527441025,1,"y5+U'-H2O"|729.31292724609375,6.610926240682602e-03,1,"b7"|795.32373046875,0.023242574185133,1,"a7+U'-H2O"|826.40509033203125,0.400069534778595,1,"y6+U'-H2O"|844.32489013671875,6.451499182730913e-03,1,"b8"|866.3614501953125,0.062791705131531,1,"ADNLDDK+U'-H2O"|884.37408447265625,7.893706671893597e-03,1,"EADNLDDK-H3N1+"|941.43206787109375,0.44364058971405,1,"y7+U'-H2O"|1012.468994140625,0.708723366260529,1,"y8+U'-H2O"|1066.4478759765625,0.035385373979807,1,"b9+U'-H2O"|1141.5120849609375,7.319674827158451e-03,1,"y9+U'-H2O"|1212.5546875,0.066727869212627,1,"[M+H]+ U'-H2O"112.050621032714844,0.028104400262237,1,"MI:C'"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O"|501.19091796875,0.035030111670494,1,"b5"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O"|584.267578125,9.894491173326969e-03,1,"LDDK+U'"|586.28167724609375,0.011093857698143,1,"a6"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]++ 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1 1 1 0 0.130456954240799 0.0 0.0 29253 7.778190140393486 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -153.0128 349541.2 874.4993 437.7533 292.1713 219.3803 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|147.112808227539063,0.358728766441345,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|431.26043701171875,0.208169266581535,1,"y4" -18.306 590.7661 Cas6e DLYQLHQGLWHLFPNR none 2 8.358111381530762 4 0.0 0 DLYQLHQGLWHLFPNR 2036.0381 0.0000 2036.0381 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.778190140393486 0 0.948040783405304 0.0 0.042552266269922 0.0 0.0 29253 5.328151996774687 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 428.2603 -420264.2 2037.0453 1019.0263 679.6866 510.0168 112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ U'-H2O"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O"|484.760772705078125,1.0,2,"[M+2H-H2O]++ U'"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]++ U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"112.051109313964844,0.062729187309742,1,"MI:C'"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'"|147.112808227539063,0.358728766441345,1,"y1"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O"|431.26043701171875,0.208169266581535,1,"y4"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]++ 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U-H3PO4"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O"|653.369873046875,0.024192033335567,1,"y5+U'-H2O"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O"|740.40380859375,0.319797694683075,1,"y6+U'-H2O"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O"129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|147.112808227539063,0.358728766441345,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|260.1971435546875,0.07334553450346,1,"y2"|431.26043701171875,0.208169266581535,1,"y4"175.119796752929688,0.014619744382799,1,"y1"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2"|229.117584228515625,0.131456702947617,1,"b2"|428.219207763671875,0.510025024414063,2,"LHQGLWH-H3N1++"|484.760772705078125,1.0,2,"LHQGLWHL-H3N1++"|520.25030517578125,0.025870239362121,1,"b4"|794.41949462890625,0.029359607025981,1,"LWHLFP"|855.42803955078125,0.362798720598221,1,"LHQGLWH-H3N1+" -25.116 508.1855 Cas5 YTPYLGR U-H3O4P1 3 30.759143829345703 1 0.637990474700928 0,0.24,0,63.80,0,0,0 YTPyLGR 868.4443 226.0590 1094.5033 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 24.764919939353597 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -142.3438 389085.8 1095.5106 548.2589 365.8417 274.6331 136.0615234375,1.0,1,"MI:A'"|136.07513427734375,0.229426234960556,1,"a1"|152.05633544921875,4.265095572918654e-03,1,"MI:G'"|158.092025756835938,9.572696872055531e-03,1,"y1-H3N1+"|164.070541381835938,3.483457025140524e-03,1,"b1"|175.119049072265625,0.031937755644321,1,"y1"|215.114288330078125,7.323490455746651e-03,1,"y2-H3N1+"|219.112014770507813,7.127284072339535e-03,1,"a2-H2O1+"|232.140228271484375,0.069322824478149,1,"y2"|237.123199462890625,0.195591405034065,1,"a2"|247.107315063476563,2.211090410128236e-03,1,"b2-H2O1+"|265.118011474609375,0.063581943511963,1,"b2"|285.1221923828125,7.153767161071301e-03,1,"PY-CO+C3O"|313.116943359375,3.152150195091963e-03,1,"PY+C3O"|327.1427001953125,1.970470184460282e-03,1,"PY-CO+U'-H2O"|328.198333740234375,2.614108612760902e-03,1,"y3-H3N1+"|329.17095947265625,0.072819426655769,2,"y5+C3O"|345.15252685546875,2.646437846124172e-03,1,"PY-CO+U'"|345.224029541015625,0.10897596180439,1,"y3"|348.06982421875,0.043133333325386,1,"MI:A"|359.1365966796875,2.3593760561198e-03,1,"b2+U'-H2O"|359.186859130859375,0.098186790943146,2,"y5+U'"|373.151611328125,2.350400667637587e-03,1,"PY+U'"|389.189697265625,2.83268908970058e-03,1,"YL+U'"|560.28369140625,0.03523913398385,1,"y4+C3O"|620.31134033203125,0.013985485769808,1,"b5-H2O1+"|657.33489990234375,0.3373843729496,1,"y5+C3O"|717.36590576171875,0.067729890346527,1,"y5+U'"|734.35107421875,3.099862718954682e-03,1,"y4+U-H3PO4"|758.38824462890625,0.013845652341843,1,"y6+C3O"|831.39337158203125,9.685350582003594e-03,1,"y5+U-H3PO4"|903.43212890625,2.896269550547004e-03,1,"[M+H-H2O]+ C3O"|921.44696044921875,0.019729314371943,1,"[M+H]+ C3O" -25.116 508.1855 Cas5 YTPYLGR U-H2O1 3 30.359920501708984 2 0.670666217803955 0,0.24,0,67.07,0,0,0 YTPyLGR 868.4443 306.0253 1174.4696 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 24.764919939353597 0 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 24.764919939353597 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -115.6884 294749.6 1175.4769 588.2421 392.4971 294.6247 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110.071525573730469,0.124598376452923,1,"iH+"|112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|204.134170532226563,0.047920491546392,1,"y2-C1H2N2+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|229.127822875976563,6.706117186695337e-03,1,"y2-H3N1+"|239.113800048828125,7.95002281665802e-03,1,"HT"|246.155319213867188,0.029895069077611,1,"y2"|286.150421142578125,0.037254326045513,1,"y3-H3N1+"|303.177154541015625,0.322829812765121,1,"y3"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|368.21673583984375,0.152305349707603,2,"y7-H2O1++"|377.221343994140625,0.194865599274635,2,"y7"|399.233306884765625,0.032629072666168,1,"y4-H3N1+"|415.200531005859375,0.011067586950958,1,"y3+U'"|416.16107177734375,9.909789077937603e-03,1,"b3"|416.2611083984375,0.390764862298965,1,"y4"|423.222259521484375,0.047973766922951,1,"TVLG+C3O"|477.163330078125,0.041644386947155,1,"a2+U-H3PO4"|499.19189453125,8.276323787868023e-03,1,"b4-H2O1+"|505.15753173828125,0.058943208307028,1,"b2+U-H3PO4"|510.177032470703125,9.497386403381825e-03,1,"b3+U'-H2O"|515.33038330078125,0.247247070074081,1,"y5"|517.205078125,0.010058866813779,1,"b4"|527.185791015625,0.053621523082256,1,"YH+U-H3PO4"|571.7821044921875,0.309090524911881,2,"y8+U-H3PO4"|598.37109375,0.028361488133669,1,"y6-H2O1+"|614.22186279296875,0.011790351010859,1,"a3+U-H3PO4"|616.3775634765625,0.524602711200714,1,"y6"|620.29071044921875,0.307169079780579,2,"[M+2H-H2O]++ U-H3PO4"|629.2969970703125,1.0,2,"[M+2H]++ U-H3PO4"|642.2138671875,0.065313711762428,1,"b3+U-H3PO4"|669.27935791015625,0.066578842699528,2,"[M+2H+U-H2O1]"|722.1842041015625,0.012603042647243,1,"b3+U-H2O"|735.421142578125,0.030300982296467,1,"y7-H2O1+"|743.26336669921875,0.047368142753839,1,"b4+U-H3PO4"|753.4393310546875,0.262213468551636,1,"y7"|814.327880859375,0.01301802136004,1,"HTVLG+U-H2O"|842.3365478515625,0.057222794741392,1,"b5+U-H3PO4"|898.3970947265625,0.025343561545014,1,"b7+U'"|909.42108154296875,0.010454332455993,1,"b8+C3O"|916.491455078125,0.011721312068403,1,"y8"|927.43896484375,0.037982285022736,1,"a6+U-H3PO4"|955.418212890625,0.050513833761215,1,"b6+U-H3PO4"|1031.5264892578125,0.180062636733055,1,"[M+H]+"|1083.4879150390625,0.025055043399334,1,"b8+U-H3PO4"|1143.546875,0.033915352076292,1,"[M+H]+ U'" -26.237 678.2844 Cas5 DYHTVLGAR U-H3O4P1 2 61.233551025390625 2 0.822381615638733 0,82.24,0,0,21.96,0,0,0,0 DyHTVLGAR 1030.5196 226.0590 1256.5786 12.389053344726563 10.107473373413086 1 1 1 0 0.218422010540962 4.155429840087891 0.046298556029797 29253 24.784701923534023 0 12.389053344726563 10.107473373413086 1 1 1 0 0.218422010540962 3.148078680038452 0.046298556029797 29253 24.784701923534023 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 -48.9879 77845.4 1257.5858 629.2966 419.8668 315.1519 110.071525573730469,0.124598376452923,1,"iH+"|112.050888061523438,0.071285061538219,1,"MI:C'"|136.0618896484375,0.444058269262314,1,"MI:A'"|136.074996948242188,0.040427405387163,1,"iY+"|152.056503295898438,0.023984039202332,1,"MI:G'"|158.092330932617188,0.029496222734451,1,"y1-H3N1+"|175.118759155273438,0.168911293148994,1,"y1"|204.134170532226563,0.047920491546392,1,"y2-C1H2N2+"|227.066131591796875,0.226746156811714,1,"MI:U-H3PO4"|229.127822875976563,6.706117186695337e-03,1,"y2-H3N1+"|239.113800048828125,7.95002281665802e-03,1,"HT"|246.155319213867188,0.029895069077611,1,"y2"|286.150421142578125,0.037254326045513,1,"y3-H3N1+"|303.177154541015625,0.322829812765121,1,"y3"|348.0694580078125,7.700511254370213e-03,1,"MI:A"|362.1336669921875,0.059144008904696,1,"iY+U-H3PO4"|368.21673583984375,0.152305349707603,2,"y7-H2O1++"|377.221343994140625,0.194865599274635,2,"y7"|399.233306884765625,0.032629072666168,1,"y4-H3N1+"|415.200531005859375,0.011067586950958,1,"y3+U'"|416.16107177734375,9.909789077937603e-03,1,"b3"|416.2611083984375,0.390764862298965,1,"y4"|423.222259521484375,0.047973766922951,1,"TVLG+C3O"|477.163330078125,0.041644386947155,1,"a2+U-H3PO4"|499.19189453125,8.276323787868023e-03,1,"b4-H2O1+"|505.15753173828125,0.058943208307028,1,"b2+U-H3PO4"|510.177032470703125,9.497386403381825e-03,1,"b3+U'-H2O"|515.33038330078125,0.247247070074081,1,"y5"|517.205078125,0.010058866813779,1,"b4"|527.185791015625,0.053621523082256,1,"YH+U-H3PO4"|571.7821044921875,0.309090524911881,2,"y8+U-H3PO4"|598.37109375,0.028361488133669,1,"y6-H2O1+"|614.22186279296875,0.011790351010859,1,"a3+U-H3PO4"|616.3775634765625,0.524602711200714,1,"y6"|620.29071044921875,0.307169079780579,2,"[M+2H-H2O]++ 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0.218422010540962 3.148078680038452 0.046298556029797 29253 24.784701923534023 0 12.389053344726563 0.0 1 1 1 0 0.218422010540962 0.0 0.0 29253 12.023569618634152 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 -162.0173 313824.7 1031.5269 516.2671 344.5138 258.6372 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-26.413 791.8590 Cse2 KSEQTTGISLGR U-H2O1 2 55.023689270019531 2 0.718522191047669 71.85,28.95,0,0,0,0,0,0,0,0,0,0 kSEQTTGISLGR 1275.6783 306.0253 1581.7036 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 52.796759224531414 0 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 52.796759224531414 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 0.0001 -0.1 1582.7109 791.8591 528.2418 396.4332 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-26.413 791.8590 Cse2 KSEQTTGISLGR none 2 31.117559432983398 3 0.0 0 KSEQTTGISLGR 1275.6783 0.0000 1275.6783 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 52.796759224531414 0 19.087356567382813 12.68174934387207 1 1 1 0 0.221869960427284 2.225220918655396 0.050896007567644 29253 52.796759224531414 0 19.087356567382813 0.0 1 1 1 0 0.221869960427284 0.0 0.0 29253 27.420436422928944 0 90.28 17.69 1.00 0.00 0.34 0.00 0.00 0.00 -153.0126 239513.9 1276.6856 638.8464 426.2334 319.9268 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112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O" -33.237 510.2805 Cas7 LLKVLK none 2 13.002236366271973 3 0.0 0 LLKVLK 712.5211 0.0000 712.5211 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 25.626236396593821 0 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 25.626236396593821 0 2.676236867904663 0.0 1 1 1 0 0.182740524411201 0.0 0.0 29253 7.604012361908893 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -153.0127 428285.7 713.5284 357.2678 238.5143 179.1376 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3" -33.237 510.2805 Cas7 KLLKVLK none 2 12.645284652709961 4 0.0 0 KLLKVLK 840.6161 0.0000 840.6161 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 25.626236396593821 0 2.676236867904663 5.566837310791016 1 1 1 0 0.182740524411201 2.118257999420166 0.3384850025177 29253 25.626236396593821 0 2.676236867904663 0.0 1 1 1 0 0.182740524411201 0.0 0.0 29253 7.604012361908893 0 3.208958625793457 0.0 0.136603727936745 0.0 0.0 29253 10.229427823002553 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -88.9652 211160.6 841.6233 421.3153 281.2126 211.1613 112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"112.050819396972656,0.010280802845955,1,"MI:C'"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O"|147.1126708984375,0.480920046567917,1,"y1"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O"|294.192901611328125,0.065465152263641,1,"KV-CO+U'-H2O"|317.22607421875,0.070976838469505,2,"a5+U'-H2O"|322.186920166015625,0.105699144303799,1,"KV+U'-H2O"|336.201568603515625,0.059393648058176,1,"LK+U'-H2O"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O"|359.2646484375,0.130350723862648,1,"y3"|404.275360107421875,0.866332650184631,2,"[M+2H]++ U'-H2O"|407.278350830078125,8.402074687182903e-03,1,"LKV-CO+U'-H2O"|435.271026611328125,0.239535450935364,1,"LKV+U'-H2O"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]++ U-H3PO4"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O"|548.35498046875,0.371608823537827,1,"b4+U'-H2O"|581.376220703125,1.0,1,"y4+U'-H2O"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O"|679.458984375,6.826628465205431e-03,1,"b5+U'"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"a2"|227.175506591796875,0.098765894770622,1,"b2"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3"129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|147.1126708984375,0.480920046567917,1,"y1"|199.180267333984375,0.547811627388001,1,"LL-CO"|227.175506591796875,0.098765894770622,1,"LL"|242.18536376953125,0.01018890645355,1,"b2"|260.19659423828125,0.163869932293892,1,"y2"|359.2646484375,0.130350723862648,1,"y3" -33.791 717.3553 Cas7 VLKEDIAAIR U-H3O4P1 2 30.723300933837891 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 226.0590 1352.7300 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -39.9831 59026.7 1353.7373 677.3723 451.9173 339.1898 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" -33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 30.485282897949219 2 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O" -33.791 717.3553 Cas7 EDIAAIR none 2 20.511859893798828 3 0.0 0 EDIAAIR 786.4236 0.0000 786.4236 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 7.072373390197754 0.0 0.099335506558418 0.0 0.0 29253 10.246214303295313 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -323.1363 819687.1 787.4308 394.2191 263.1485 197.6132 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"130.049942016601563,0.014329176396132,1,"b1"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|543.36065673828125,0.106723681092262,1,"y5"|658.3885498046875,0.117386691272259,1,"y6" -33.791 717.3553 Cas7 VLKEDIAAIR none 2 19.036767959594727 4 0.0 0 VLKEDIAAIR 1126.6710 0.0000 1126.6710 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 2.145905494689941 0.031824681907892 29253 19.699521215489526 0 7.072373390197754 0.0 0.099335506558418 0.0 0.0 29253 10.246214303295313 0 9.227341651916504 0.0 1 1 1 0 0.158668205142021 0.0 0.0 29253 10.246214303295313 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 -153.0126 271134.1 1127.6783 564.3428 376.5643 282.6750 112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ U'-H2O"112.050666809082031,0.246375799179077,1,"MI:C'"|129.10223388671875,0.102737873792648,1,"iK(C6H13N2O)"|136.061660766601563,1.0,1,"MI:A'"|136.074462890625,0.05758473277092,1,"iK(C5H10N1)C3O"|152.0562744140625,0.090718396008015,1,"MI:G'"|158.091842651367188,0.067611984908581,1,"y1-H3N1+"|175.118728637695313,0.241062179207802,1,"y1"|178.097976684570313,0.103741243481636,1,"iK(C5H10N1)U'-H2O"|185.164260864257813,0.064587898552418,1,"a2"|288.202667236328125,0.059821642935276,1,"y2"|317.217132568359375,0.017043316736817,1,"y3-C1H2N2+"|348.06854248046875,0.020584469661117,1,"MI:A"|352.1593017578125,0.017145426943898,1,"KE+U'-H2O"|359.238128662109375,0.050968244671822,1,"y3"|430.276580810546875,0.0471286252141,1,"y4"|435.271270751953125,0.12653174996376,1,"IAAI-CO+U'-H2O"|505.274322509765625,0.617979943752289,2,"y8+U'-H2O"|543.36065673828125,0.106723681092262,1,"y5"|561.81707763671875,0.270584404468536,2,"y9+U'-H2O"|611.35137939453125,0.919540822505951,2,"[M+2H]++ U'-H2O"|658.3885498046875,0.117386691272259,1,"y6"|679.3475341796875,0.030254062265158,1,"EDIAAI-CO+U'-H2O"|787.42864990234375,0.330469816923142,1,"y7"|863.4605712890625,0.020168174058199,1,"b7+U'-H2O"|1009.53955078125,0.027259975671768,1,"y8+U'-H2O"|1221.7052001953125,0.016711112111807,1,"[M+H]+ 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1.844556570053101 184.46,126.75,97.82,0,0,32.15,32.15,0,0,0,0,0 mATSGMMTELGK 1255.5611 226.0590 1481.6200 19.278144836425781 14.91402530670166 1 1 1 0 0.371337056159973 4.102765560150146 0.158967092633247 29253 47.324498821223671 0 5.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -48.9889 66039.0 1482.6273 741.8173 494.8806 371.4123 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H2O1+"|953.44305419921875,0.880237638950348,1,"y9"|1036.4752197265625,0.154976740479469,1,"y10-H2O1+"|1037.4661865234375,0.044277537614107,1,"y10-H3N1+"|1054.489013671875,0.891642868518829,1,"y10"|1107.508056640625,0.010800593532622,1,"y11-H2O1+"|1125.5260009765625,0.135128006339073,1,"y11" -34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U-H2O1 2 32.330818176269531 1 0.536135375499725 0,0,0,53.61,0,0,0,0,6.09 MVFcLSAGK 970.4616 306.0253 1276.4869 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -9.0052 14087.1 1277.4942 639.2507 426.5029 320.1290 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O" -34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK UU-H2O1 2 31.977167129516602 2 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 612.0506 1582.5122 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 144.0075 -181767.2 1583.5195 792.2634 528.5114 396.6353 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U" -34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK none 2 21.468671798706055 3 0.0 0 MVFCLSAGK 970.4616 0.0000 970.4616 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 7.007274678147403 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -162.0178 333206.8 971.4689 486.2381 324.4945 243.6227 112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"y7+U'"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"112.050895690917969,0.209176629781723,1,"MI:C'"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O"|147.112640380859375,0.216315641999245,1,"y1"|152.056716918945313,0.298746705055237,1,"MI:G'"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5"|630.2962646484375,0.098198756575584,1,"y6+C3O"|688.197998046875,0.013070179149508,1,"FCL+U"|690.31988525390625,0.040793959051371,1,"y6+U'"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3"|884.31402587890625,0.01827629096806,1,"y6+U-H2O"|902.33062744140625,0.050201874226332,1,"y6+U"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3"|1031.390869140625,0.102401345968246,1,"y7+U-H2O"|1049.4049072265625,0.163576155900955,1,"y7+U"120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|147.112640380859375,0.216315641999245,1,"y1"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2"|219.116134643554688,0.69442480802536,1,"a2"|247.111434936523438,0.152931392192841,1,"b2"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|362.202789306640625,0.197416797280312,1,"y4"|394.17913818359375,0.058901127427816,1,"b3"|475.288665771484375,0.123156972229481,1,"y5" -34.072 648.2559 Cse2 HQQALLRMVFCLSAGK none 2 16.85017204284668 4 0.0 0 HQQALLRMVFCLSAGK 1800.9491 0.0000 1800.9491 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 7.007274678147403 0 5.535978317260742 0.0 0.133406266570091 0.0 0.0 29253 5.499638206201645 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 253.2259 -280899.6 1801.9564 901.4818 601.3237 451.2446 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-36.767 933.9406 Cas7 TLALLSGKSVDEAEK U-H3O4P1 2 38.031223297119141 1 0.146051496267319 0,0,0,0,0,0,0,14.61,0,0,0,0,0,0,14.61 TLALLSGkSVDEAEk 1559.8407 226.0590 1785.8996 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 30.20450085062139 0 100.00 19.27 98.86 2.97 4.81 0.00 0.00 0.00 -39.9835 44726.4 1786.9069 893.9571 596.3072 447.4822 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ U'-H2O"|868.406494140625,0.043710377067328,1,"LSGKSVDE+C3O"|878.50921630859375,0.04271687194705,1,"b8+U'-H2O"|881.51123046875,0.10030597448349,1,"LALLSGK-CO+U-H3PO4"|997.42559814453125,0.045007601380348,1,"SGKSVDEAE+U'-H2O"|1056.4964599609375,0.445992678403854,1,"y9+U'-H2O"|1143.5274658203125,0.826412320137024,1,"y10+U'-H2O"|1179.6209716796875,0.033004622906446,1,"b11+U'-H2O"|1256.603515625,0.408009380102158,1,"y11+U'-H2O"|1369.7083740234375,0.034444786608219,1,"a14-H3N1+"|1440.7257080078125,0.081928692758083,1,"b12+U-H3PO4" -36.767 933.9406 Cas7 TLALLSGKSVDEAEK U-H2O1 2 37.87286376953125 2 0.146051496267319 0,0,0,0,0,0,0,14.61,0,0,0,0,0,0,14.61 TLALLSGkSVDEAEk 1559.8407 306.0253 1865.8660 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 30.20450085062139 0 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 30.20450085062139 0 100.00 19.27 98.86 2.97 4.81 0.00 0.00 0.00 -0.0004 0.4 1866.8732 933.9403 622.9626 467.4738 112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ U'-H2O"|868.406494140625,0.043710377067328,1,"LSGKSVDE+C3O"|878.50921630859375,0.04271687194705,1,"b8+U'-H2O"|881.51123046875,0.10030597448349,1,"LALLSGK-CO+U-H3PO4"|997.42559814453125,0.045007601380348,1,"SGKSVDEAE+U'-H2O"|1056.4964599609375,0.445992678403854,1,"y9+U'-H2O"|1143.5274658203125,0.826412320137024,1,"y10+U'-H2O"|1179.6209716796875,0.033004622906446,1,"b11+U'-H2O"|1256.603515625,0.408009380102158,1,"y11+U'-H2O"|1369.7083740234375,0.034444786608219,1,"a14-H3N1+"|1440.7257080078125,0.081928692758083,1,"b12+U-H3PO4"112.050788879394531,0.988550662994385,1,"MI:C'"|129.102310180664063,0.19722355902195,1,"y1-H2O1+"|130.086502075195313,0.048023488372564,1,"y1-H3N1+"|136.061859130859375,1.0,1,"MI:A'"|136.074386596679688,0.043711859732866,1,"iK(C5H10N1)C3O"|147.112518310546875,0.193087175488472,1,"y1"|152.057113647460938,0.048149388283491,1,"MI:G'"|178.097366333007813,0.102339640259743,1,"iK(C5H10N1)U'-H2O"|185.128814697265625,0.083276964724064,1,"LA"|187.143661499023438,0.23836749792099,1,"a2"|215.13873291015625,0.321440905332565,1,"b2"|258.14697265625,0.041196417063475,1,"LSG"|286.17620849609375,0.71120023727417,1,"b3"|347.191192626953125,0.092741332948208,1,"y3"|348.071380615234375,0.086939558386803,1,"MI:A"|371.26641845703125,0.093694075942039,1,"a4"|381.24774169921875,0.102398455142975,1,"b4-H2O1+"|399.261932373046875,0.237983465194702,1,"b4"|428.24981689453125,0.035399843007326,1,"LSGKS-CO-H3N1+"|476.235626220703125,0.134913399815559,1,"y4"|494.3353271484375,0.033407032489777,1,"b5-H2O1+"|572.26702880859375,0.285636007785797,2,"y10+U'-H2O"|591.26123046875,0.143231973052025,1,"y5"|628.81036376953125,0.243827223777771,2,"y11+U'-H2O"|685.353759765625,0.270588964223862,2,"a14-H3N1++"|690.33538818359375,0.044740207493305,1,"y6"|720.873046875,0.314045906066895,2,"b12+U-H3PO4"|777.35723876953125,0.164657771587372,1,"y7"|827.93499755859375,0.630500316619873,2,"[M+2H]++ U'-H2O"|868.406494140625,0.043710377067328,1,"LSGKSVDE+C3O"|878.50921630859375,0.04271687194705,1,"b8+U'-H2O"|881.51123046875,0.10030597448349,1,"LALLSGK-CO+U-H3PO4"|934.4134521484375,0.175290405750275,1,"a7+U-H2O"|997.42559814453125,0.045007601380348,1,"SGKSVDEAE+U'-H2O"|1056.4964599609375,0.445992678403854,1,"y9+U'-H2O"|1143.5274658203125,0.826412320137024,1,"y10+U'-H2O"|1179.6209716796875,0.033004622906446,1,"b11+U'-H2O"|1256.603515625,0.408009380102158,1,"y11+U'-H2O"|1369.7083740234375,0.034444786608219,1,"a14-H3N1+"|1440.7257080078125,0.081928692758083,1,"b12+U-H3PO4" -36.767 933.9406 Cas7 TLALLSGKSVDEAEK none 2 24.814916610717774 3 0.0 0 TLALLSGKSVDEAEK 1559.8407 0.0000 1559.8407 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 30.20450085062139 0 10.280866622924805 6.024999141693115 1 1 1 0 0.165740802884102 1.043980240821838 0.130615994334221 29253 30.20450085062139 0 10.280866622924805 0.0 1 1 1 0 0.165740802884102 0.0 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-37.098 735.8139 Cse1 ALYTFAEGFK UU-H3O4P1 2 72.032722473144531 2 1.608833074569702 2.46,0,0,72.55,107.41,132.71,0,158.96,160.88,0 ALYTFAEGfK 1145.5757 532.0843 1677.6600 15.1768798828125 9.408187866210938 1 1 1 0 0.253406018018723 0.0 0.118536047637463 29253 30.293854786395897 0 15.1768798828125 9.408187866210938 1 1 1 0 0.253406018018723 0.0 0.118536047637463 29253 30.293854786395897 0 99.17 12.14 50.50 9.25 4.24 0.00 0.00 0.00 104.0234 -123861.3 1678.6673 839.8373 560.2273 420.4223 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U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" -39.118 623.2540 Cse2 MLTWWGK UU-H3O4P1 2 36.48870849609375 2 1.08866548538208 0,0.95,0,108.87,16.34,0,7.64 MLTwWGK 920.4578 532.0843 1452.5421 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 104.0244 -143032.4 1453.5494 727.2783 485.1880 364.1428 112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U"112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U" -39.118 623.2540 Cas6e VPLIKEAEQIAWLQR none 2 17.291851043701172 3 0.0 0 VPLIKEAEQIAWLQR 1793.0200 0.0000 1793.0200 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 4.992705345153809 0.0 0.040718141943216 0.0 0.0 29253 8.25391312848474 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 274.2633 -305580.0 1794.0272 897.5173 598.6806 449.2623 112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ U'"|1096.445556640625,0.048582393676043,1,"y6+U-H2O"|1114.4610595703125,0.042080584913492,1,"y6+U"112.050796508789063,0.103300340473652,1,"MI:C'"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O"|147.112686157226563,0.124614141881466,1,"y1"|152.056869506835938,0.015434425324202,1,"MI:G'"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2"|245.132080078125,0.17075103521347,1,"b2"|346.179931640625,0.042745251208544,1,"b3"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4"|390.2135009765625,0.532232463359833,1,"y3"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4"|457.197662353515625,0.010401514358819,1,"WW-CO+U'"|465.1192626953125,0.018610520288348,1,"iW+U-H2O"|483.1278076171875,0.129291772842407,1,"iW+U"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O"|584.17132568359375,0.068149335682392,1,"TW-CO+U"|594.158447265625,0.032711785286665,1,"TW+U-H2O"|612.1688232421875,0.057017870247364,1,"TW+U"|669.20440673828125,0.012318334542215,1,"WW-CO+U"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4"|789.36456298828125,0.076395474374294,1,"y5+U'"|798.2451171875,0.01280861068517,1,"TWW+U"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4"|882.31549072265625,0.055004987865686,1,"y4+U-H2O"|900.32177734375,0.064147591590881,1,"y4+U"|902.44384765625,0.015058934688568,1,"y6+U'"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4"|983.36517333984375,0.134756237268448,1,"y5+U-H2O"|1001.3760986328125,0.190459117293358,1,"y5+U"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+ 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112.051109313964844,0.062729187309742,1,"MI:C'+"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'+"|147.112808227539063,0.358728766441345,1,"y1+"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O+"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2+"|229.117584228515625,0.131456702947617,1,"b2+"|260.1971435546875,0.07334553450346,1,"y2+"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O+"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O++"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O++"|431.26043701171875,0.208169266581535,1,"y4+"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]+U'-H2O++"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O+"|484.760772705078125,1.0,2,"[M+2H-H2O]+U'++"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]+U-H3PO4++"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O+"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O+"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O+"|653.369873046875,0.024192033335567,1,"y5+U'-H2O+"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O+"|740.40380859375,0.319797694683075,1,"y6+U'-H2O+"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O+"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O+"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O+"112.051109313964844,0.062729187309742,1,"MI:C'+"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'+"|147.112808227539063,0.358728766441345,1,"y1+"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O+"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2+"|229.117584228515625,0.131456702947617,1,"b2+"|260.1971435546875,0.07334553450346,1,"y2+"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O+"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O++"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O++"|431.26043701171875,0.208169266581535,1,"y4+"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]+U'-H2O++"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O+"|484.760772705078125,1.0,2,"[M+2H-H2O]+U'++"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]+U-H3PO4++"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O+"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O+"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O+"|653.369873046875,0.024192033335567,1,"y5+U'-H2O+"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O+"|740.40380859375,0.319797694683075,1,"y6+U'-H2O+"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O+"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O+"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O+"129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|147.112808227539063,0.358728766441345,1,"y1+"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2+"|229.117584228515625,0.131456702947617,1,"b2+"|260.1971435546875,0.07334553450346,1,"y2+"|431.26043701171875,0.208169266581535,1,"y4+" +18.306 590.7661 Cas6e DLYQLHQGLWHLFPNR none 2 8.358111381530762 4 0.0 0 DLYQLHQGLWHLFPNR 2036.0381 0.0000 2036.0381 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.778190140393486 0 0.948040783405304 0.0 0.042552266269922 0.0 0.0 29253 5.328151996774687 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 428.2603 -420264.2 2037.0453 1019.0263 679.6866 510.0168 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112.050895690917969,0.209176629781723,1,"MI:C'+"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'+"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O+"|147.112640380859375,0.216315641999245,1,"y1+"|152.056716918945313,0.298746705055237,1,"MI:G'+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+"|630.2962646484375,0.098198756575584,1,"y6+C3O+"|690.31988525390625,0.040793959051371,1,"y6+U'+"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4+"|837.3975830078125,0.075952410697937,1,"y7+U'+"|884.31402587890625,0.01827629096806,1,"y6+U-H2O+"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4+"|1031.390869140625,0.102401345968246,1,"y7+U-H2O+" +34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK UU-H2O1 2 31.977167129516602 2 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 612.0506 1582.5122 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 144.0075 -181767.2 1583.5195 792.2634 528.5114 396.6353 112.050895690917969,0.209176629781723,1,"MI:C'+"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'+"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O+"|147.112640380859375,0.216315641999245,1,"y1+"|152.056716918945313,0.298746705055237,1,"MI:G'+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+"|630.2962646484375,0.098198756575584,1,"y6+C3O+"|690.31988525390625,0.040793959051371,1,"y6+U'+"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4+"|837.3975830078125,0.075952410697937,1,"y7+U'+"|884.31402587890625,0.01827629096806,1,"y6+U-H2O+"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4+"|1031.390869140625,0.102401345968246,1,"y7+U-H2O+"112.050895690917969,0.209176629781723,1,"MI:C'+"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'+"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O+"|147.112640380859375,0.216315641999245,1,"y1+"|152.056716918945313,0.298746705055237,1,"MI:G'+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+"|630.2962646484375,0.098198756575584,1,"y6+C3O+"|688.197998046875,0.013070179149508,1,"FCL+U+"|690.31988525390625,0.040793959051371,1,"y6+U'+"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4+"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3+"|884.31402587890625,0.01827629096806,1,"y6+U-H2O+"|902.33062744140625,0.050201874226332,1,"y6+U+"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4+"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3+"|1031.390869140625,0.102401345968246,1,"y7+U-H2O+"|1049.4049072265625,0.163576155900955,1,"y7+U+" +34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK none 2 21.468671798706055 3 0.0 0 MVFCLSAGK 970.4616 0.0000 970.4616 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 7.007274678147403 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -162.0178 333206.8 971.4689 486.2381 324.4945 243.6227 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112.050796508789063,0.103300340473652,1,"MI:C'+"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'+"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O+"|147.112686157226563,0.124614141881466,1,"y1+"|152.056869506835938,0.015434425324202,1,"MI:G'+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2+"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2+"|245.132080078125,0.17075103521347,1,"b2+"|346.179931640625,0.042745251208544,1,"b3+"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4++"|390.2135009765625,0.532232463359833,1,"y3+"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4+"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4++"|457.197662353515625,0.010401514358819,1,"WW-CO+U'+"|465.1192626953125,0.018610520288348,1,"iW+U-H2O++"|483.1278076171875,0.129291772842407,1,"iW+U++"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4+"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4+"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O+"|584.17132568359375,0.068149335682392,1,"TW-CO+U+"|594.158447265625,0.032711785286665,1,"TW+U-H2O+"|612.1688232421875,0.057017870247364,1,"TW+U+"|669.20440673828125,0.012318334542215,1,"WW-CO+U+"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4+"|789.36456298828125,0.076395474374294,1,"y5+U'+"|798.2451171875,0.01280861068517,1,"TWW+U+"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4+"|882.31549072265625,0.055004987865686,1,"y4+U-H2O+"|900.32177734375,0.064147591590881,1,"y4+U+"|902.44384765625,0.015058934688568,1,"y6+U'+"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4+"|983.36517333984375,0.134756237268448,1,"y5+U-H2O+"|1001.3760986328125,0.190459117293358,1,"y5+U+"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+U'+"|1096.445556640625,0.048582393676043,1,"y6+U-H2O+"|1114.4610595703125,0.042080584913492,1,"y6+U+"112.050796508789063,0.103300340473652,1,"MI:C'+"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'+"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O+"|147.112686157226563,0.124614141881466,1,"y1+"|152.056869506835938,0.015434425324202,1,"MI:G'+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2+"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2+"|245.132080078125,0.17075103521347,1,"b2+"|346.179931640625,0.042745251208544,1,"b3+"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4++"|390.2135009765625,0.532232463359833,1,"y3+"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4+"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4++"|457.197662353515625,0.010401514358819,1,"WW-CO+U'+"|465.1192626953125,0.018610520288348,1,"iW+U-H2O++"|483.1278076171875,0.129291772842407,1,"iW+U++"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4+"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4+"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O+"|584.17132568359375,0.068149335682392,1,"TW-CO+U+"|594.158447265625,0.032711785286665,1,"TW+U-H2O+"|612.1688232421875,0.057017870247364,1,"TW+U+"|669.20440673828125,0.012318334542215,1,"WW-CO+U+"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4+"|789.36456298828125,0.076395474374294,1,"y5+U'+"|798.2451171875,0.01280861068517,1,"TWW+U+"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4+"|882.31549072265625,0.055004987865686,1,"y4+U-H2O+"|900.32177734375,0.064147591590881,1,"y4+U+"|902.44384765625,0.015058934688568,1,"y6+U'+"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4+"|983.36517333984375,0.134756237268448,1,"y5+U-H2O+"|1001.3760986328125,0.190459117293358,1,"y5+U+"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+U'+"|1096.445556640625,0.048582393676043,1,"y6+U-H2O+"|1114.4610595703125,0.042080584913492,1,"y6+U+" 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112.050796508789063,0.103300340473652,1,"MI:C'+"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'+"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O+"|147.112686157226563,0.124614141881466,1,"y1+"|152.056869506835938,0.015434425324202,1,"MI:G'+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2+"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2+"|245.132080078125,0.17075103521347,1,"b2+"|346.179931640625,0.042745251208544,1,"b3+"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4++"|390.2135009765625,0.532232463359833,1,"y3+"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4+"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4++"|457.197662353515625,0.010401514358819,1,"WW-CO+U'+"|465.1192626953125,0.018610520288348,1,"iW+U-H2O++"|483.1278076171875,0.129291772842407,1,"iW+U++"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4+"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4+"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O+"|584.17132568359375,0.068149335682392,1,"TW-CO+U+"|594.158447265625,0.032711785286665,1,"TW+U-H2O+"|612.1688232421875,0.057017870247364,1,"TW+U+"|669.20440673828125,0.012318334542215,1,"WW-CO+U+"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4+"|789.36456298828125,0.076395474374294,1,"y5+U'+"|798.2451171875,0.01280861068517,1,"TWW+U+"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4+"|882.31549072265625,0.055004987865686,1,"y4+U-H2O+"|900.32177734375,0.064147591590881,1,"y4+U+"|902.44384765625,0.015058934688568,1,"y6+U'+"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4+"|983.36517333984375,0.134756237268448,1,"y5+U-H2O+"|1001.3760986328125,0.190459117293358,1,"y5+U+"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+U'+"|1096.445556640625,0.048582393676043,1,"y6+U-H2O+"|1114.4610595703125,0.042080584913492,1,"y6+U+"112.050796508789063,0.103300340473652,1,"MI:C'+"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'+"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O+"|147.112686157226563,0.124614141881466,1,"y1+"|152.056869506835938,0.015434425324202,1,"MI:G'+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2+"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2+"|245.132080078125,0.17075103521347,1,"b2+"|346.179931640625,0.042745251208544,1,"b3+"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4++"|390.2135009765625,0.532232463359833,1,"y3+"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4+"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4++"|457.197662353515625,0.010401514358819,1,"WW-CO+U'+"|465.1192626953125,0.018610520288348,1,"iW+U-H2O++"|483.1278076171875,0.129291772842407,1,"iW+U++"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4+"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4+"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O+"|584.17132568359375,0.068149335682392,1,"TW-CO+U+"|594.158447265625,0.032711785286665,1,"TW+U-H2O+"|612.1688232421875,0.057017870247364,1,"TW+U+"|669.20440673828125,0.012318334542215,1,"WW-CO+U+"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4+"|789.36456298828125,0.076395474374294,1,"y5+U'+"|798.2451171875,0.01280861068517,1,"TWW+U+"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4+"|882.31549072265625,0.055004987865686,1,"y4+U-H2O+"|900.32177734375,0.064147591590881,1,"y4+U+"|902.44384765625,0.015058934688568,1,"y6+U'+"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4+"|983.36517333984375,0.134756237268448,1,"y5+U-H2O+"|1001.3760986328125,0.190459117293358,1,"y5+U+"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+U'+"|1096.445556640625,0.048582393676043,1,"y6+U-H2O+"|1114.4610595703125,0.042080584913492,1,"y6+U+"129.102279663085938,0.140630826354027,1,"iK(C6H13N2O)"|155.080978393554688,0.011355513706803,1,"AE-CO-H2O1+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2+"|175.118576049804688,0.053739137947559,1,"y1+"|183.076873779296875,0.014720181003213,1,"AE-H2O1+"|185.128158569335938,0.063421830534935,1,"IA"|197.129074096679688,0.016815194860101,1,"b2+"|241.079193115234375,0.010938653722405,1,"EQ-H3N1+"|258.10791015625,0.013713601976633,1,"EQ"|312.116729736328125,0.013135173358023,1,"EAE-H2O1+"|416.2613525390625,0.013992154970765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From c2e9fd7e0f869dede535557bb5f5975a09fa0350 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 23 Jan 2025 14:37:35 +0100 Subject: [PATCH 326/471] remove annotation of internal ions (to many duplicated m/z) --- .../ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp | 55 ++++++- src/tests/topp/OpenNuXL_1_output.idXML | 66 ++++---- src/tests/topp/OpenNuXL_2_output.idXML | 66 ++++---- src/tests/topp/OpenNuXL_3_output.idXML | 76 ++++----- src/tests/topp/OpenNuXL_3_output2.tsv | 50 +++--- src/tests/topp/OpenNuXL_4_output.idXML | 74 ++++----- src/tests/topp/OpenNuXL_4_output2.tsv | 48 +++--- src/tests/topp/OpenNuXL_5_output.idXML | 66 ++++---- src/tests/topp/OpenNuXL_6_output.idXML | 120 +++++++------- src/tests/topp/OpenNuXL_6_output2.tsv | 150 +++++++++--------- 10 files changed, 408 insertions(+), 363 deletions(-) diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp index 19bb64501a7..646c1251b61 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp @@ -27,8 +27,6 @@ using namespace std; namespace OpenMS { - static const std::regex trailing_charge_pattern_rx(R"(\++$)"); // match one or more '+' characters at the end of the string - // create total loss spectrum using new_param as template static PeakSpectrum createTotalLossSpectrumForAnnotations(const AASequence& fixed_and_variable_modified_peptide, size_t precursor_charge, Param new_param) { @@ -68,6 +66,47 @@ namespace OpenMS return total_loss_spectrum; } + /** + @brief Removes duplicate peaks based on their m/z values. + + This function identifies and removes duplicate peaks from the spectrum based on + their m/z values. Only the first occurrence of a peak with a given m/z value is + retained. The function uses the `select()` method to efficiently remove the + duplicate peaks and their corresponding entries in the data arrays. + + @note The spectrum should be sorted by position (m/z) before calling this function + to ensure correct identification of duplicates. + */ + static void removeDuplicatedPeaks(MSSpectrum& spec) + { + if (spec.empty()) return; + + std::vector indices_to_keep; + indices_to_keep.push_back(0); // Always keep the first peak + + for (Size i = 1; i < spec.size(); ++i) + { + // Compare the current peak's m/z with the last kept peak's m/z + if (spec[i].getMZ() != spec[indices_to_keep.back()].getMZ()) + { + indices_to_keep.push_back(i); + } +#ifdef DEBUG_OpenNuXL + else + { + // happens a lot with precursor peaks and internal ions + std::cout << "Removing duplicate peak at m/z: " << spec[i].getMZ() << endl; + std::cout << spec.getStringDataArrays()[0][i] << " - " + << spec.getStringDataArrays()[0][indices_to_keep.back()] << std::endl; + } +#endif + } + + if (indices_to_keep.size() == spec.size()) return; // No duplicates found + + spec.select(indices_to_keep); + } + using MapIonIndexToFragmentAnnotation = map >; // ion centric (e.g. b and y-ion) spectrum annotation for unshifted ions (will later be merged with shifted) @@ -283,7 +322,7 @@ namespace OpenMS param.setValue("add_x_ions", "false"); param.setValue("add_y_ions", "true"); param.setValue("add_z_ions", "false"); - param.setValue("add_internal_fragments", "true"); + param.setValue("add_internal_fragments", "false"); // TODO: creates too many ions with identical masses partial_loss_spectrum_generator.setParameters(param); #ifdef _OPENMP #pragma omp parallel for @@ -304,7 +343,7 @@ namespace OpenMS a.best_localization = unmodified_sequence; a.best_localization_score = 0; - AASequence aas(AASequence::fromString(unmodified_sequence)); + AASequence aas(unmodified_sequence); // reapply modifications (because for memory reasons we only stored the index and recreation is fast) vector all_modified_peptides; @@ -427,6 +466,8 @@ namespace OpenMS partial_loss_spectrum.sortByPosition(); // need to resort after adding marker ions + + // ion centric (e.g. b and y-ion) spectrum annotation that records all shifts of specific ions (e.g. y5, y5 + U, y5 + C3O) MapIonIndexToFragmentAnnotation shifted_b_ions, shifted_y_ions, shifted_a_ions; vector shifted_immonium_ions, annotated_marker_ions; @@ -438,7 +479,11 @@ namespace OpenMS alignment.clear(); ppm_error_array.clear(); - // align spectra (only allow matching charges) + + // remove duplicate peaks to prevent non-deterministic annotations (e.g., [M+H-H2O]+U and [M+H]+U-H2O ) + removeDuplicatedPeaks(partial_loss_spectrum); + + // align spectra (only allow matching charges) OPXLSpectrumProcessingAlgorithms::getSpectrumAlignmentFastCharge(alignment, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, diff --git a/src/tests/topp/OpenNuXL_1_output.idXML b/src/tests/topp/OpenNuXL_1_output.idXML index ace5a147fb7..b85061b2a3d 100644 --- a/src/tests/topp/OpenNuXL_1_output.idXML +++ b/src/tests/topp/OpenNuXL_1_output.idXML @@ -6,7 +6,7 @@ - + @@ -32,7 +32,7 @@ - + @@ -70,7 +70,7 @@ - + @@ -112,7 +112,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -272,7 +272,7 @@ - + @@ -309,8 +309,8 @@ - - + + @@ -352,7 +352,7 @@ - + @@ -389,8 +389,8 @@ - - + + @@ -432,7 +432,7 @@ - + @@ -512,7 +512,7 @@ - + @@ -592,7 +592,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -752,7 +752,7 @@ - + @@ -789,8 +789,8 @@ - - + + @@ -832,7 +832,7 @@ - + @@ -869,8 +869,8 @@ - - + + @@ -912,7 +912,7 @@ - + @@ -949,8 +949,8 @@ - - + + @@ -992,7 +992,7 @@ - + @@ -1072,7 +1072,7 @@ - + @@ -1232,7 +1232,7 @@ - + @@ -1269,8 +1269,8 @@ - - + + @@ -1312,7 +1312,7 @@ - + @@ -1392,7 +1392,7 @@ - + @@ -1472,7 +1472,7 @@ - + @@ -1552,7 +1552,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_2_output.idXML b/src/tests/topp/OpenNuXL_2_output.idXML index cb531638ad2..58c27d9f2ad 100644 --- a/src/tests/topp/OpenNuXL_2_output.idXML +++ b/src/tests/topp/OpenNuXL_2_output.idXML @@ -6,7 +6,7 @@ - + @@ -32,7 +32,7 @@ - + @@ -70,7 +70,7 @@ - + @@ -112,7 +112,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -272,7 +272,7 @@ - + @@ -309,8 +309,8 @@ - - + + @@ -352,7 +352,7 @@ - + @@ -389,8 +389,8 @@ - - + + @@ -432,7 +432,7 @@ - + @@ -512,7 +512,7 @@ - + @@ -592,7 +592,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -752,7 +752,7 @@ - + @@ -789,8 +789,8 @@ - - + + @@ -832,7 +832,7 @@ - + @@ -869,8 +869,8 @@ - - + + @@ -912,7 +912,7 @@ - + @@ -949,8 +949,8 @@ - - + + @@ -992,7 +992,7 @@ - + @@ -1072,7 +1072,7 @@ - + @@ -1232,7 +1232,7 @@ - + @@ -1269,8 +1269,8 @@ - - + + @@ -1312,7 +1312,7 @@ - + @@ -1392,7 +1392,7 @@ - + @@ -1472,7 +1472,7 @@ - + @@ -1552,7 +1552,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_3_output.idXML b/src/tests/topp/OpenNuXL_3_output.idXML index 47c5e988a6d..66b29bc9904 100644 --- a/src/tests/topp/OpenNuXL_3_output.idXML +++ b/src/tests/topp/OpenNuXL_3_output.idXML @@ -6,7 +6,7 @@ - + @@ -44,7 +44,7 @@ - + @@ -82,7 +82,7 @@ - + @@ -124,7 +124,7 @@ - + @@ -204,7 +204,7 @@ - + @@ -284,7 +284,7 @@ - + @@ -321,8 +321,8 @@ - - + + @@ -364,7 +364,7 @@ - + @@ -401,8 +401,8 @@ - - + + @@ -444,7 +444,7 @@ - + @@ -520,7 +520,7 @@ - + @@ -596,7 +596,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -748,7 +748,7 @@ - + @@ -824,7 +824,7 @@ - + @@ -896,7 +896,7 @@ - + @@ -976,7 +976,7 @@ - + @@ -1052,7 +1052,7 @@ - + @@ -1128,7 +1128,7 @@ - + @@ -1165,8 +1165,8 @@ - - + + @@ -1208,7 +1208,7 @@ - + @@ -1245,8 +1245,8 @@ - - + + @@ -1288,7 +1288,7 @@ - + @@ -1325,8 +1325,8 @@ - - + + @@ -1368,7 +1368,7 @@ - + @@ -1448,7 +1448,7 @@ - + @@ -1608,7 +1608,7 @@ - + @@ -1645,8 +1645,8 @@ - - + + @@ -1688,7 +1688,7 @@ - + @@ -1840,7 +1840,7 @@ - + @@ -1920,7 +1920,7 @@ - + @@ -2000,7 +2000,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_3_output2.tsv b/src/tests/topp/OpenNuXL_3_output2.tsv index 37c9406d0e4..b29657d3230 100644 --- a/src/tests/topp/OpenNuXL_3_output2.tsv +++ b/src/tests/topp/OpenNuXL_3_output2.tsv @@ -1,27 +1,27 @@ #RT m/z proteins peptide NA charge score rank best localization score localization scores best localization(s) peptide weight NA weight cross-link weight NuXL:total_loss_score NuXL:partial_loss_score CountSequenceIsTop CountSequenceCharges CountSequenceIsXL CountSequenceIsPeptide NuXL:MIC NuXL:pl_pc_MIC NuXL:pl_MIC nr_candidates -ln(poisson) isotope_error A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H fragment_annotation -17.788 712.7828 Cas7 AEADNLDDKK U-H2O1 2 69.974990844726563 1 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 306.0253 1423.5504 11.444543838500977 16.099458694458008 1 1 1 0 0.216474175453186 0.0 0.394327819347382 3 315.0 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 112.050621032714844,0.028104400262237,1,"MI:C'+"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'+"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1+"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2+"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O+"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2+"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3+"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3+"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O+"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'+"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O+"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4+"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O++"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O+"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O+"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4+"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O++"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O+"|501.19091796875,0.035030111670494,1,"b5+"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O++"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O+"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O+"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O++"|584.267578125,9.894491173326969e-03,1,"LDDK+U'+"|586.28167724609375,0.011093857698143,1,"a6+"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]+U'-H2O++"|599.27777099609375,0.764611601829529,1,"y4+U'-H2O+"|606.77734375,0.299497008323669,2,"[M+2H]+U'-H2O++"|614.27984619140625,0.039939478039742,1,"b6+"|680.2978515625,0.018134105950594,1,"a6+U'-H2O+"|698.31036376953125,6.59028347581625e-03,1,"LDDK+U-H3PO4+"|712.36236572265625,0.394213527441025,1,"y5+U'-H2O+"|729.31292724609375,6.610926240682602e-03,1,"b7+"|795.32373046875,0.023242574185133,1,"a7+U'-H2O+"|826.40509033203125,0.400069534778595,1,"y6+U'-H2O+"|844.32489013671875,6.451499182730913e-03,1,"b8+"|866.3614501953125,0.062791705131531,1,"ADNLDDK+U'-H2O+"|884.37408447265625,7.893706671893597e-03,1,"EADNLDDK-H3N1+"|941.43206787109375,0.44364058971405,1,"y7+U'-H2O+"|1012.468994140625,0.708723366260529,1,"y8+U'-H2O+"|1066.4478759765625,0.035385373979807,1,"b9+U'-H2O+"|1141.5120849609375,7.319674827158451e-03,1,"y9+U'-H2O+"|1212.5546875,0.066727869212627,1,"[M+H]+U'-H2O+" -18.306 590.7661 Cas6e LDSKGNIK U-H2O1 2 25.741664886474609 1 2.196093797683716 0,0,0,219.61,0,0,0,8.00 LDSkGNIK 873.4920 306.0253 1179.5173 2.428377628326416 4.320775508880615 1 1 1 0 0.130456954240799 0.0 0.175812318921089 1 315.0 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 112.051109313964844,0.062729187309742,1,"MI:C'+"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'+"|147.112808227539063,0.358728766441345,1,"y1+"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O+"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2+"|229.117584228515625,0.131456702947617,1,"b2+"|260.1971435546875,0.07334553450346,1,"y2+"|310.150909423828125,0.016878057271242,1,"SK+U'-H2O+"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O++"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O++"|431.26043701171875,0.208169266581535,1,"y4+"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]+U'-H2O++"|481.21795654296875,0.062367469072342,1,"SKGN+U'-H2O+"|484.760772705078125,1.0,2,"[M+2H-H2O]+U'++"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]+U-H3PO4++"|594.3009033203125,0.063189655542374,1,"SKGNI+U'-H2O+"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O+"|596.24334716796875,0.02193003334105,1,"DSKGN+U'-H2O+"|653.369873046875,0.024192033335567,1,"y5+U'-H2O+"|709.32696533203125,0.225882858037949,1,"DSKGNI+U'-H2O+"|740.40380859375,0.319797694683075,1,"y6+U'-H2O+"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O+"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O+"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O+" -25.116 508.1855 Cas5 YTPYLGR AU 3 40.562583923339844 1 0.734427034854889 0,0.24,0,73.44,0,0,0 YTPyLGR 868.4443 653.0884 1521.5327 3.710045576095581 2.351816177368164 1 1 1 0 0.190965637564659 0.0 0.210292190313339 1 315.0 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -0.0007 1.3 1522.5400 761.7736 508.1848 381.3905 136.0615234375,1.0,1,"MI:A'+"|136.07513427734375,0.229426234960556,1,"a1+"|152.05633544921875,4.265095572918654e-03,1,"MI:G'+"|158.092025756835938,9.572696872055531e-03,1,"y1-H3N1+"|164.070541381835938,3.483457025140524e-03,1,"b1+"|175.119049072265625,0.031937755644321,1,"y1+"|215.114288330078125,7.323490455746651e-03,1,"y2-H3N1+"|219.112014770507813,7.127284072339535e-03,1,"a2-H2O1+"|232.140228271484375,0.069322824478149,1,"y2+"|237.123199462890625,0.195591405034065,1,"a2+"|247.107315063476563,2.211090410128236e-03,1,"b2-H2O1+"|265.118011474609375,0.063581943511963,1,"b2+"|285.1221923828125,7.153767161071301e-03,1,"PY-CO+C3O+"|313.116943359375,3.152150195091963e-03,1,"PY+C3O+"|327.1427001953125,1.970470184460282e-03,1,"PY-CO+U'-H2O+"|328.198333740234375,2.614108612760902e-03,1,"y3-H3N1+"|329.17095947265625,0.072819426655769,2,"y5+C3O++"|345.15252685546875,2.646437846124172e-03,1,"PY-CO+U'+"|345.224029541015625,0.10897596180439,1,"y3+"|348.06982421875,0.043133333325386,1,"MI:A+"|359.1365966796875,2.3593760561198e-03,1,"b2+U'-H2O+"|359.186859130859375,0.098186790943146,2,"y5+U'++"|373.151611328125,2.350400667637587e-03,1,"PY+U'+"|389.189697265625,2.83268908970058e-03,1,"YL+U'+"|456.184844970703125,0.019872423261404,2,"y5+U-H2O++"|465.191619873046875,0.025686334818602,2,"y5+U++"|560.28369140625,0.03523913398385,1,"y4+C3O+"|620.31134033203125,0.013985485769808,1,"b5-H2O1+"|657.33489990234375,0.3373843729496,1,"y5+C3O+"|717.36590576171875,0.067729890346527,1,"y5+U'+"|734.35107421875,3.099862718954682e-03,1,"y4+U-H3PO4+"|758.38824462890625,0.013845652341843,1,"y6+C3O+"|831.39337158203125,9.685350582003594e-03,1,"y5+U-H3PO4+"|849.408447265625,4.016013350337744e-03,1,"y5+U-HPO3+"|903.43212890625,2.896269550547004e-03,1,"[M+H-H2O]+C3O+"|911.36871337890625,0.012803317978978,1,"y5+U-H2O+"|921.44696044921875,0.019729314371943,1,"[M+H]+C3O+"|929.37530517578125,0.034058455377817,1,"y5+U+" -26.237 678.2844 Cas5 DYHTVLGAR U 2 67.563796997070313 1 0.892229020595551 0,89.22,0,0,23.58,0,0,0,0 DyHTVLGAR 1030.5196 324.0359 1354.5555 12.389053344726563 8.871867179870606 1 1 1 0 0.218422010540962 0.0 0.070792749524117 3 315.0 0 44.41 9.78 7.13 0.00 2.40 0.00 0.00 0.00 0.0006 -0.9 1355.5627 678.2850 452.5258 339.6461 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-33.791 717.3553 Cas7 VLKEDIAAIR U-H2O1 2 31.678943634033203 1 1.077150344848633 0,0,107.72,0,0,0,0,0,0,0 VLkEDIAAIR 1126.6710 306.0253 1432.6963 9.227341651916504 1.977586507797241 1 1 1 0 0.158668205142021 0.0 0.059569962322712 2 315.0 0 100.00 20.31 24.64 0.00 9.07 0.00 0.00 0.00 0.0001 -0.1 1433.7036 717.3554 478.5727 359.1814 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-34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U 2 37.691276550292969 1 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 324.0359 1294.4975 6.533727645874023 1.259999871253967 1 1 1 0 0.223560705780983 0.0 0.098648108541965 2 315.0 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 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+34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U 2 37.691276550292969 1 0.762710511684418 0,0,0,76.27,0,0,0,0,6.09 MVFcLSAGK 970.4616 324.0359 1294.4975 6.533727645874023 1.259999871253967 1 1 1 0 0.223560705780983 0.0 0.098648108541965 2 315.0 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 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37.098 735.8139 Cse1 ALYTFAEGFK U 2 76.229042053222656 1 1.608833074569702 2.46,0,0,72.55,107.41,132.71,0,158.96,160.88,0 ALYTFAEGfK 1145.5757 324.0359 1469.6116 15.1768798828125 9.470569610595703 1 1 1 0 0.253406018018723 0.0 0.216487392783165 1 315.0 0 99.17 12.14 50.50 9.25 4.24 0.00 0.00 0.00 -0.0008 1.1 1470.6189 735.8131 490.8778 368.4102 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-37.536 833.8672 Cse2 LVQPFGWENPR U 2 52.818855285644531 1 5.590284824371338 8.97,0,0,0,0,0,559.03,0,0,0,0 LVQPFGwENPR 1341.6830 324.0359 1665.7188 5.432636737823486 5.498913288116455 1 1 1 0 0.222448781132698 0.0 0.252318680286407 1 315.0 0 47.85 8.60 8.42 0.00 4.17 0.00 0.00 0.00 -0.0005 0.7 1666.7261 833.8667 556.2469 417.4370 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-37.864 698.2974 Cas5 DEPMITLPR U 2 67.925018310546875 1 0.827892243862152 0,0,82.79,0,0,0,0,12.18,0 DEpMITLPR 1070.5430 324.0359 1394.5789 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 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-37.864 698.2974 DECOY_Cse1 PMVNDNILR U 2 39.625930786132813 2 0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 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112.050773620605469,0.042819745838642,1,"MI:C'+"|136.061843872070313,0.196844235062599,1,"MI:A'+"|152.056671142578125,0.023113740608096,1,"MI:G'+"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1+"|182.092300415039063,0.052632980048656,1,"iP+U'++"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2+"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2+"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2+"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|348.068084716796875,9.060680866241455e-03,1,"MI:A+"|376.089996337890625,0.029012143611908,1,"iP+U-H2O++"|385.25506591796875,0.261529922485352,1,"y3+"|394.095611572265625,0.040202785283327,1,"iP+U++"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O+"|454.151214599609375,0.077750355005264,1,"b3+U'+"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4+"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|567.26251220703125,0.116328254342079,2,"y7+U-H2O++"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U++"|585.19580078125,8.00114031881094e-03,1,"b4+U'+"|599.387451171875,0.483213186264038,1,"y5+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]+U-H3PO4++"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O+"|649.3082275390625,0.248698011040688,2,"[M+2H]+U-H3PO4++"|669.29034423828125,0.01186771504581,1,"b6-H2O1+"|699.23114013671875,0.020817343145609,1,"b4+U-H3PO4+"|730.42572021484375,0.26859325170517,1,"y6+"|782.404296875,0.012716175056994,1,"EPMITLP"|784.31610107421875,7.947030477225781e-03,1,"a5+U-H3PO4+"|812.31365966796875,0.012815644964576,1,"b5+U-H3PO4+"|825.46112060546875,0.037652637809515,1,"y5+U-H3PO4+"|827.4814453125,0.037520926445723,1,"y7+"|842.45953369140625,0.042362816631794,1,"y6+U'+"|879.48016357421875,0.099386416375637,1,"y7+C3O+"|939.5068359375,0.254053741693497,1,"y8-H3N1+"|956.483642578125,0.047358602285385,1,"y6+U-H3PO4+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1071.533935546875,0.012802372686565,1,"[M+H]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4+"|1133.5010986328125,0.05346042662859,1,"y7+U-H2O+"|1151.51953125,0.053188119083643,1,"y7+U+"|1183.5704345703125,0.054004456847906,1,"[M+H]+U'+" +37.864 698.2974 DECOY_Cse1 PMVNDNILR U 2 39.625930786132813 2 0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 112.050773620605469,0.042819745838642,1,"MI:C'+"|136.061843872070313,0.196844235062599,1,"MI:A'+"|152.056671142578125,0.023113740608096,1,"MI:G'+"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1+"|182.092300415039063,0.052632980048656,1,"iP+U'++"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2+"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2+"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2+"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|348.068084716796875,9.060680866241455e-03,1,"MI:A+"|376.089996337890625,0.029012143611908,1,"iP+U-H2O++"|385.25506591796875,0.261529922485352,1,"y3+"|394.095611572265625,0.040202785283327,1,"iP+U++"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O+"|454.151214599609375,0.077750355005264,1,"b3+U'+"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4+"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|567.26251220703125,0.116328254342079,2,"y7+U-H2O++"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U++"|585.19580078125,8.00114031881094e-03,1,"b4+U'+"|599.387451171875,0.483213186264038,1,"y5+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]+U-H3PO4++"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O+"|649.3082275390625,0.248698011040688,2,"[M+2H]+U-H3PO4++"|669.29034423828125,0.01186771504581,1,"b6-H2O1+"|699.23114013671875,0.020817343145609,1,"b4+U-H3PO4+"|730.42572021484375,0.26859325170517,1,"y6+"|782.404296875,0.012716175056994,1,"EPMITLP"|784.31610107421875,7.947030477225781e-03,1,"a5+U-H3PO4+"|812.31365966796875,0.012815644964576,1,"b5+U-H3PO4+"|825.46112060546875,0.037652637809515,1,"y5+U-H3PO4+"|827.4814453125,0.037520926445723,1,"y7+"|842.45953369140625,0.042362816631794,1,"y6+U'+"|879.48016357421875,0.099386416375637,1,"y7+C3O+"|939.5068359375,0.254053741693497,1,"y8-H3N1+"|956.483642578125,0.047358602285385,1,"y6+U-H3PO4+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1071.533935546875,0.012802372686565,1,"[M+H]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4+"|1133.5010986328125,0.05346042662859,1,"y7+U-H2O+"|1151.51953125,0.053188119083643,1,"y7+U+"|1183.5704345703125,0.054004456847906,1,"[M+H]+U'+"112.050773620605469,0.042819745838642,1,"MI:C'+"|136.061843872070313,0.196844235062599,1,"MI:A'+"|152.056671142578125,0.023113740608096,1,"MI:G'+"|153.1024169921875,0.012729996815324,1,"a2-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1+"|182.092300415039063,0.052632980048656,1,"a1+U'+"|227.065277099609375,0.01328039355576,1,"MI:U-H3PO4+"|245.076187133789063,0.142766728997231,1,"MI:U-HPO3+"|253.100723266601563,9.467311203479767e-03,1,"a2+C3O+"|281.09564208984375,9.001040831208229e-03,1,"b2+C3O+"|288.20294189453125,8.992226794362068e-03,1,"y2+"|296.12347412109375,0.02242861315608,1,"a1+U-H3PO4+"|313.13702392578125,0.016673086211085,1,"a2+U'+"|341.126983642578125,0.080299213528633,1,"b2+U'+"|348.068084716796875,9.060680866241455e-03,1,"MI:A+"|376.089996337890625,0.029012143611908,1,"a1+U-H2O+"|394.095611572265625,0.040202785283327,1,"a1+U+"|427.164215087890625,0.022860564291477,1,"a2+U-H3PO4+"|525.14324951171875,0.028857138007879,1,"a2+U+"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"b2+U-H2O+"|553.13372802734375,0.032937977463007,1,"b2+U+"|553.27215576171875,0.012286836281419,1,"NDNIL-H3N1+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]+U-H3PO4++"|649.3082275390625,0.248698011040688,2,"[M+2H]+U-H3PO4++"|669.29034423828125,0.01186771504581,1,"MVNDNI-H2O1+"|825.46112060546875,0.037652637809515,1,"y7-H2O1+"|956.483642578125,0.047358602285385,1,"y8-H2O1+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4+"|1183.5704345703125,0.054004456847906,1,"[M+H]+U'+" +39.118 623.2540 Cse2 MLTWWGK U 2 48.237815856933594 1 1.08866548538208 0,0.95,0,108.87,16.34,0,7.64 MLTwWGK 920.4578 324.0359 1244.4937 3.611835241317749 2.463027238845825 1 1 1 0 0.372912466526032 0.0 0.215587794780731 2 315.0 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 112.050796508789063,0.103300340473652,1,"MI:C'+"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'+"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O+"|147.112686157226563,0.124614141881466,1,"y1+"|152.056869506835938,0.015434425324202,1,"MI:G'+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2+"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2+"|245.132080078125,0.17075103521347,1,"b2+"|346.179931640625,0.042745251208544,1,"b3+"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4++"|390.2135009765625,0.532232463359833,1,"y3+"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4+"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4++"|465.1192626953125,0.018610520288348,1,"iW+U-H2O++"|483.1278076171875,0.129291772842407,1,"iW+U++"|789.36456298828125,0.076395474374294,1,"y5+U'+"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4+"|882.31549072265625,0.055004987865686,1,"y4+U-H2O+"|900.32177734375,0.064147591590881,1,"y4+U+"|902.44384765625,0.015058934688568,1,"y6+U'+"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4+"|983.36517333984375,0.134756237268448,1,"y5+U-H2O+"|1001.3760986328125,0.190459117293358,1,"y5+U+"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+U'+"|1096.445556640625,0.048582393676043,1,"y6+U-H2O+"|1114.4610595703125,0.042080584913492,1,"y6+U+" +39.853 861.3889 Cas5 LAGPMQAWGQPTFEGTRPTGR U 3 37.401420593261719 1 2.457196474075317 0,0,0,0,0,0,0,0,244.47,0,0,0,0,0,0,0,0,0,245.72,0,0 LAGPMQAWGQPTFEGTRPtGR 2257.1062 324.0359 2581.1421 9.457996368408203 11.046560287475586 1 1 1 0 0.13300721347332 0.0 0.168000027537346 2 315.0 0 14.94 3.38 3.08 0.00 1.95 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 112.050376892089844,0.03075241483748,1,"MI:C'+"|127.086822509765625,0.084323570132256,1,"GP-CO"|136.061492919921875,0.149392291903496,1,"MI:A'+"|152.056304931640625,0.019498618319631,1,"MI:G'+"|153.101638793945313,0.027191694825888,1,"PM-CO-C1H4S1+"|155.081680297851563,0.129901498556137,1,"GP"|157.1085205078125,0.016523864120245,1,"y1-H2O1+"|157.133346557617188,0.116147078573704,1,"a2+"|158.092391967773438,0.186959013342857,1,"y1-H3N1+"|172.1072998046875,0.019877409562469,1,"QA-CO"|175.118942260742188,0.864344000816345,1,"y1+"|185.128372192382813,0.101255014538765,1,"b2+"|200.10223388671875,0.099220559000969,1,"QA"|226.117660522460938,0.046638753265142,1,"AGP"|228.13330078125,0.014135158620775,1,"PTG-CO"|229.09967041015625,0.03934133425355,1,"PM"|230.129501342773438,9.715269319713116e-03,1,"AW-CO"|232.1397705078125,0.013686842285097,1,"y2+"|242.149429321289063,0.073746532201767,1,"b3+"|260.10400390625,0.014170597307384,1,"MQ"|281.159515380859375,0.051366787403822,1,"AGPM-CO-C1H4S1+"|286.121002197265625,0.049559332430363,1,"GPM"|303.146270751953125,0.076557174324989,3,"b8+C3O+++"|313.1822509765625,8.80386121571064e-03,1,"TRP-C1H2N2+"|315.144927978515625,0.083149679005146,1,"AWG"|329.163055419921875,0.014427128247917,1,"AGPM-CO"|331.139739990234375,0.012301723472774,1,"MQA"|357.157958984375,0.112319760024548,1,"AGPM"|370.20562744140625,0.010619016364217,1,"GTRP-C1H2N2+"|372.708740234375,0.117013581097126,2,"y7++"|386.179534912109375,0.045954059809446,1,"QAW"|394.2432861328125,0.019391525536776,1,"a5-C1H4S1+"|397.153350830078125,0.014580637216568,1,"GPMQ-H3N1+"|414.1788330078125,0.048771116882563,1,"GPMQ"|426.172393798828125,0.011522333137691,1,"AWGQ-H3N1+"|428.194000244140625,0.016342636197805,1,"PMQA"|430.24169921875,0.102167457342148,1,"y4+"|443.201904296875,0.046294238418341,1,"QAWG"|468.190093994140625,0.045015033334494,1,"AGPMQ-H3N1+"|485.219146728515625,0.061722680926323,1,"AGPMQ"|570.2940673828125,0.015357924625278,1,"GTRPTG"|577.2655029296875,0.01251458004117,1,"y3+U-HPO3+"|581.27789306640625,0.01857952028513,1,"b6-H3N1+"|582.268798828125,0.013687066733837,1,"b5+U'+"|598.30841064453125,0.012375350110233,1,"b6+"|609.81640625,0.391953557729721,2,"y11++"|660.29052734375,0.011049717664719,1,"GQPTFE"|665.32275390625,0.049633823335171,2,"y12-H3N1++"|670.325927734375,0.010814912617207,1,"FEGTRP-H2O1+"|671.30474853515625,0.033622957766056,1,"GPMQAW"|673.8443603515625,0.12153934687376,2,"y12++"|699.315185546875,0.014566479250789,1,"GQPTFEG-H2O1+"|702.3807373046875,0.015244751237333,1,"y7-C1H2N2+"|728.35498046875,0.048261545598507,2,"y13+C3O++"|744.40643310546875,0.051093131303787,1,"y7+"|758.361328125,0.14195054769516,2,"y13+U'++"|767.34393310546875,0.093842588365078,3,"y19+U-H3PO4+++"|774.99993896484375,0.047129739075899,3,"y18+U-H2O+++"|781.00018310546875,0.071356788277626,3,"y18+U+++"|782.33447265625,0.026894029229879,1,"AGPMQAWG-H3N1+"|815.3856201171875,0.147706180810928,2,"b13+U-HPO3++"|851.41131591796875,0.183295845985413,2,"y14+U'++"|862.4254150390625,0.215514808893204,1,"TFEGTRPT-CO"|886.9246826171875,0.320382863283157,2,"y15+U'++"|899.40863037109375,0.029477229341865,2,"b15+U-H3PO4++"|908.42529296875,0.371884346008301,2,"y14+U-H3PO4++"|942.45684814453125,0.053394634276628,1,"PTFEGTRPT-CO-H3N1+"|943.94268798828125,0.374551713466644,2,"y15+U-H3PO4++"|951.449951171875,0.069044589996338,2,"y17-H2O1++"|953.4407958984375,0.018099347129464,1,"GPMQAWGQP"|957.4124755859375,0.12921978533268,2,"y14+U++"|983.93023681640625,0.169056877493858,2,"y15+U-H2O++"|992.9346923828125,0.170678496360779,2,"y15+U++"|1000.46746826171875,0.030669666826725,1,"QAWGQPTFE-CO-H3N1+"|1007.9669189453125,0.198151588439941,2,"y16+U-H3PO4++"|1113.4766845703125,0.044029250741005,2,"y17+U-H2O++"|1122.482666015625,0.080889888107777,2,"y17+U++" +40.038 1043.4525 Cas7 SGYYAQNIGESSLRTIHLAQLR GU-H2O1 3 12.18718147277832 1 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 4.506982803344727 0.042108997702599 1 1 1 0 0.193572551012039 0.0 2.997914329171181e-03 1 315.0 0 11.70 1.76 0.00 0.00 0.89 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 129.066375732421875,0.011452200822532,1,"SS-CO-H2O1+"|136.062057495117188,0.117006808519363,1,"MI:A'+"|136.075942993164063,0.061224263161421,1,"iY+"|147.076553344726563,0.033742658793926,1,"SS-CO"|152.05645751953125,8.929258212447167e-03,1,"MI:G'+"|157.10845947265625,0.019333818927407,1,"y1-H2O1+"|158.092269897460938,0.014068718068302,1,"y1-H3N1+"|175.11895751953125,1.0,1,"y1+"|200.10223388671875,0.037957575172186,1,"AQ"|200.13934326171875,0.015138491056859,1,"NI-CO"|207.112930297851563,0.018860274925828,1,"YA-CO"|227.066238403320313,0.013174916617572,1,"MI:U-H3PO4+"|228.134735107421875,0.140522807836533,1,"NI"|235.107940673828125,0.038548536598682,1,"YA"|242.149642944335938,0.085332110524178,1,"SSL-CO-H2O1+"|258.1038818359375,0.021212872117758,1,"ESS-CO-H2O1+"|271.17724609375,0.036110296845436,1,"y2-H3N1+"|288.20263671875,0.540427029132843,1,"y2+"|313.187530517578125,0.047560345381498,1,"LAQ"|352.200225830078125,0.011090287938714,1,"TIH"|371.19293212890625,0.051817037165165,1,"ESSL-CO-H2O1+"|398.252685546875,0.013688288629055,1,"y3-H2O1+"|399.237579345703125,0.012889615260065,1,"y3-H3N1+"|416.261444091796875,0.611584186553955,1,"y3+"|427.2349853515625,0.017148498445749,1,"AQNI"|428.2210693359375,0.057390972971916,1,"IGESS-CO-H2O1+"|470.27783203125,0.012210931628942,1,"y4-H3N1+"|487.298919677734375,0.575224339962006,1,"y4+"|514.23504638671875,0.032693766057491,1,"a5+"|541.30743408203125,0.047687828540802,1,"IGESSL-CO-H2O1+"|542.22161865234375,0.017067449167371,1,"b5+"|573.2657470703125,0.016528343781829,1,"YAQNI-H3N1+"|596.27105712890625,0.011223017238081,1,"AQNIGE-H3N1+"|613.29095458984375,0.011800601147115,1,"GESSLR-H3N1+"|630.299072265625,0.011752335354686,1,"YAQNIG-H3N1+"|636.37835693359375,0.014756876043975,1,"TIHLAQ-CO"|647.3037109375,0.027322037145495,1,"YAQNIG"|655.31170654296875,0.017578417435288,1,"AQNIGES-CO-H3N1+"|672.33526611328125,0.207145139575005,1,"AQNIGES-CO"|888.46136474609375,0.064613588154316,1,"NIGESSLRT-CO-C1H2N2+"|967.49603271484375,0.044361278414726,1,"QNIGESSLR-H2O1+"|985.50390625,0.146545097231865,1,"QNIGESSLR"|1042.531005859375,0.303900748491287,1,"QNIGESSLRT-C1H2N1O1+"|1221.4688720703125,0.043008159846067,1,"b8+U+" diff --git a/src/tests/topp/OpenNuXL_4_output.idXML b/src/tests/topp/OpenNuXL_4_output.idXML index 5e240a7af06..98ffde099db 100644 --- a/src/tests/topp/OpenNuXL_4_output.idXML +++ b/src/tests/topp/OpenNuXL_4_output.idXML @@ -6,7 +6,7 @@ - + @@ -44,7 +44,7 @@ - + @@ -82,7 +82,7 @@ - + @@ -124,7 +124,7 @@ - + @@ -204,7 +204,7 @@ - + @@ -284,7 +284,7 @@ - + @@ -321,8 +321,8 @@ - - + + @@ -364,7 +364,7 @@ - + @@ -401,8 +401,8 @@ - - + + @@ -444,7 +444,7 @@ - + @@ -520,7 +520,7 @@ - + @@ -596,7 +596,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -748,7 +748,7 @@ - + @@ -824,7 +824,7 @@ - + @@ -904,7 +904,7 @@ - + @@ -980,7 +980,7 @@ - + @@ -1056,7 +1056,7 @@ - + @@ -1093,8 +1093,8 @@ - - + + @@ -1136,7 +1136,7 @@ - + @@ -1173,8 +1173,8 @@ - - + + @@ -1216,7 +1216,7 @@ - + @@ -1253,8 +1253,8 @@ - - + + @@ -1296,7 +1296,7 @@ - + @@ -1376,7 +1376,7 @@ - + @@ -1536,7 +1536,7 @@ - + @@ -1573,8 +1573,8 @@ - - + + @@ -1616,7 +1616,7 @@ - + @@ -1768,7 +1768,7 @@ - + @@ -1848,7 +1848,7 @@ - + @@ -1928,7 +1928,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_4_output2.tsv b/src/tests/topp/OpenNuXL_4_output2.tsv index cafb0fec2bd..bc58d22f6da 100644 --- a/src/tests/topp/OpenNuXL_4_output2.tsv +++ b/src/tests/topp/OpenNuXL_4_output2.tsv @@ -1,26 +1,26 @@ #RT m/z proteins peptide NA charge score rank best localization score localization scores best localization(s) peptide weight NA weight cross-link weight NuXL:total_loss_score NuXL:partial_loss_score CountSequenceIsTop CountSequenceCharges CountSequenceIsXL CountSequenceIsPeptide NuXL:MIC NuXL:pl_pc_MIC NuXL:pl_MIC nr_candidates -ln(poisson) isotope_error A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H fragment_annotation -17.788 712.7828 Cas7 AEADNLDDKK U-H2O1 2 69.974990844726563 1 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 306.0253 1423.5504 11.444543838500977 16.099458694458008 1 1 1 0 0.216474175453186 0.0 0.394327819347382 3 315.0 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 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112.050819396972656,0.010280802845955,1,"MI:C'+"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'+"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O+"|147.1126708984375,0.480920046567917,1,"y1+"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O+"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O++"|199.180267333984375,0.547811627388001,1,"a2+"|227.175506591796875,0.098765894770622,1,"b2+"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2+"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O++"|317.22607421875,0.070976838469505,2,"a5+U'-H2O++"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O++"|359.2646484375,0.130350723862648,1,"y3+"|404.275360107421875,0.866332650184631,2,"[M+2H]+U'-H2O++"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O+"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O+"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]+U-H3PO4++"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O+"|548.35498046875,0.371608823537827,1,"b4+U'-H2O+"|581.376220703125,1.0,1,"y4+U'-H2O+"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O+"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O+"|679.458984375,6.826628465205431e-03,1,"b5+U'+"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O+" +33.237 510.2805 DECOY_Cas7 LKLLVK U-H2O1 2 30.675045013427734 2 1.106894612312317 0,110.69,77.01,0,0,27.74 LkLLVK 712.5211 306.0253 1018.5464 2.676236867904663 4.84662389755249 1 1 1 0 0.182740524411201 0.0 0.375015050172806 2 315.0 0 1.17647397518158 4.721068859100342 0.079879306256771 0.0 0.211029142141342 2 315.0 0 11.44 0.77 1.03 0.00 0.00 0.00 0.00 0.00 -0.0000 0.1 1019.5537 510.2805 340.5227 255.6439 112.050819396972656,0.010280802845955,1,"MI:C'+"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'+"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O+"|147.1126708984375,0.480920046567917,1,"y1+"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O+"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O++"|199.180267333984375,0.547811627388001,1,"a2+"|227.175506591796875,0.098765894770622,1,"b2+"|242.18536376953125,0.01018890645355,1,"y2-H2O1+"|260.19659423828125,0.163869932293892,1,"y2+"|291.191192626953125,0.036187149584293,2,"y4+U'-H2O++"|317.22607421875,0.070976838469505,2,"a5+U'-H2O++"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O++"|359.2646484375,0.130350723862648,1,"y3+"|404.275360107421875,0.866332650184631,2,"[M+2H]+U'-H2O++"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O+"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O+"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]+U-H3PO4++"|520.3590087890625,0.078761622309685,1,"a4+U'-H2O+"|548.35498046875,0.371608823537827,1,"b4+U'-H2O+"|581.376220703125,1.0,1,"y4+U'-H2O+"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O+"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O+"|679.458984375,6.826628465205431e-03,1,"b5+U'+"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O+"112.050819396972656,0.010280802845955,1,"MI:C'+"|129.102203369140625,0.27744522690773,1,"y1-H2O1+"|130.086227416992188,0.285412341356277,1,"y1-H3N1+"|136.061920166015625,0.114355176687241,1,"MI:A'+"|136.074798583984375,0.016609838232398,1,"iK(C5H10N1)C3O+"|147.1126708984375,0.480920046567917,1,"y1+"|178.097457885742188,0.216726034879684,1,"iK(C5H10N1)U'-H2O+"|195.1241455078125,0.044040825217962,1,"iK+U'-H2O++"|199.180267333984375,0.547811627388001,1,"LL-CO"|227.175506591796875,0.098765894770622,1,"LL"|242.18536376953125,0.01018890645355,1,"b2+"|317.22607421875,0.070976838469505,2,"a5+U'-H2O++"|336.201568603515625,0.059393648058176,1,"b2+U'-H2O+"|347.733367919921875,0.167680993676186,2,"y5+U'-H2O++"|359.2646484375,0.130350723862648,1,"y3+"|404.275360107421875,0.866332650184631,2,"[M+2H]+U'-H2O++"|449.286956787109375,0.375419855117798,1,"b3+U'-H2O+"|453.2811279296875,0.016704117879272,1,"y3+U'-H2O+"|461.292083740234375,0.053712595254183,2,"[M+2H-H2O]+U-H3PO4++"|520.3590087890625,0.078761622309685,1,"b4+C3O+"|562.3695068359375,0.036407515406609,1,"b4+U'-H2O+"|633.44268798828125,0.025088682770729,1,"a5+U'-H2O+"|661.44122314453125,0.17664310336113,1,"b5+U'-H2O+"|679.458984375,6.826628465205431e-03,1,"b5+U'+"|694.46063232421875,0.589181542396545,1,"y5+U'-H2O+" 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+34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK U 2 37.691276550292969 1 0.762710511684418 0,0,0,76.27,0,0,0,0,6.09 MVFcLSAGK 970.4616 324.0359 1294.4975 6.533727645874023 1.259999871253967 1 1 1 0 0.223560705780983 0.0 0.098648108541965 2 315.0 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 0.0001 -0.2 1295.5048 648.2560 432.5064 324.6316 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-37.864 698.2974 Cas5 DEPMITLPR U 2 67.925018310546875 1 0.827892243862152 0,0,82.79,0,0,0,0,12.18,0 DEpMITLPR 1070.5430 324.0359 1394.5789 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 -0.0006 0.9 1395.5862 698.2967 465.8669 349.6520 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-37.864 698.2974 DECOY_Cse1 PMVNDNILR U 2 39.625930786132813 2 0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 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112.050773620605469,0.042819745838642,1,"MI:C'+"|136.061843872070313,0.196844235062599,1,"MI:A'+"|152.056671142578125,0.023113740608096,1,"MI:G'+"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1+"|182.092300415039063,0.052632980048656,1,"iP+U'++"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2+"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2+"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2+"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|348.068084716796875,9.060680866241455e-03,1,"MI:A+"|376.089996337890625,0.029012143611908,1,"iP+U-H2O++"|385.25506591796875,0.261529922485352,1,"y3+"|394.095611572265625,0.040202785283327,1,"iP+U++"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O+"|454.151214599609375,0.077750355005264,1,"b3+U'+"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4+"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|567.26251220703125,0.116328254342079,2,"y7+U-H2O++"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U++"|585.19580078125,8.00114031881094e-03,1,"b4+U'+"|599.387451171875,0.483213186264038,1,"y5+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]+U-H3PO4++"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O+"|649.3082275390625,0.248698011040688,2,"[M+2H]+U-H3PO4++"|669.29034423828125,0.01186771504581,1,"b6-H2O1+"|699.23114013671875,0.020817343145609,1,"b4+U-H3PO4+"|730.42572021484375,0.26859325170517,1,"y6+"|782.404296875,0.012716175056994,1,"EPMITLP"|784.31610107421875,7.947030477225781e-03,1,"a5+U-H3PO4+"|812.31365966796875,0.012815644964576,1,"b5+U-H3PO4+"|825.46112060546875,0.037652637809515,1,"y5+U-H3PO4+"|827.4814453125,0.037520926445723,1,"y7+"|842.45953369140625,0.042362816631794,1,"y6+U'+"|879.48016357421875,0.099386416375637,1,"y7+C3O+"|939.5068359375,0.254053741693497,1,"y8-H3N1+"|956.483642578125,0.047358602285385,1,"y6+U-H3PO4+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1071.533935546875,0.012802372686565,1,"[M+H]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4+"|1133.5010986328125,0.05346042662859,1,"y7+U-H2O+"|1151.51953125,0.053188119083643,1,"y7+U+"|1183.5704345703125,0.054004456847906,1,"[M+H]+U'+" +37.864 698.2974 DECOY_Cse1 PMVNDNILR U 2 39.625930786132813 2 0.374298125505447 37.43,23.00,0,0,0,0,0,0,0 pMVNDNILR 1070.5543 324.0359 1394.5901 9.885402679443359 5.683440685272217 1 1 1 0 0.331657320261002 0.0 0.142823621630669 3 315.0 0 0.837916910648346 0.834788680076599 0.017832582816482 0.0 0.049031101167202 3 315.0 0 19.68 3.37 4.28 0.00 2.31 0.00 0.00 0.00 0.0050 -7.1 1395.5974 698.3023 465.8707 349.6548 112.050773620605469,0.042819745838642,1,"MI:C'+"|136.061843872070313,0.196844235062599,1,"MI:A'+"|152.056671142578125,0.023113740608096,1,"MI:G'+"|153.1024169921875,0.012729996815324,1,"PM-CO-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1+"|182.092300415039063,0.052632980048656,1,"iP+U'++"|199.071426391601563,0.058049991726875,1,"a2-H2O1+"|215.137588500976563,7.142127025872469e-03,1,"IT"|217.081710815429688,0.353501588106155,1,"a2+"|217.134567260742188,6.709000561386347e-03,1,"MI-CO"|227.065277099609375,0.01328039355576,1,"b2-H2O1+"|245.076187133789063,0.142766728997231,1,"b2+"|254.16058349609375,7.313383277505636e-03,1,"y2-H2O1+"|255.144805908203125,0.087086223065853,1,"y2-H3N1+"|272.171295166015625,0.502800464630127,1,"y2+"|296.12347412109375,0.02242861315608,1,"a3-H2O1+"|348.068084716796875,9.060680866241455e-03,1,"MI:A+"|376.089996337890625,0.029012143611908,1,"iP+U-H2O++"|385.25506591796875,0.261529922485352,1,"y3+"|394.095611572265625,0.040202785283327,1,"iP+U++"|427.164215087890625,0.022860564291477,1,"a4-H2O1+"|436.14556884765625,0.01471087988466,1,"b3+U'-H2O+"|454.151214599609375,0.077750355005264,1,"b3+U'+"|470.25738525390625,0.382063090801239,2,"y8-H3N1++"|486.30303955078125,0.700427412986755,1,"y4+"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|540.25250244140625,8.27430747449398e-03,1,"a5-H2O1+"|567.26251220703125,0.116328254342079,2,"y7+U-H2O++"|568.24761962890625,0.028157891705632,1,"b5-H2O1+"|576.2607421875,0.211633667349815,2,"y7+U++"|585.19580078125,8.00114031881094e-03,1,"b4+U'+"|599.387451171875,0.483213186264038,1,"y5+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]+U-H3PO4++"|648.1551513671875,7.638523355126381e-03,1,"b3+U-H2O+"|649.3082275390625,0.248698011040688,2,"[M+2H]+U-H3PO4++"|669.29034423828125,0.01186771504581,1,"b6-H2O1+"|699.23114013671875,0.020817343145609,1,"b4+U-H3PO4+"|730.42572021484375,0.26859325170517,1,"y6+"|782.404296875,0.012716175056994,1,"EPMITLP"|784.31610107421875,7.947030477225781e-03,1,"a5+U-H3PO4+"|812.31365966796875,0.012815644964576,1,"b5+U-H3PO4+"|825.46112060546875,0.037652637809515,1,"y5+U-H3PO4+"|827.4814453125,0.037520926445723,1,"y7+"|842.45953369140625,0.042362816631794,1,"y6+U'+"|879.48016357421875,0.099386416375637,1,"y7+C3O+"|939.5068359375,0.254053741693497,1,"y8-H3N1+"|956.483642578125,0.047358602285385,1,"y6+U-H3PO4+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1071.533935546875,0.012802372686565,1,"[M+H]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4+"|1133.5010986328125,0.05346042662859,1,"y7+U-H2O+"|1151.51953125,0.053188119083643,1,"y7+U+"|1183.5704345703125,0.054004456847906,1,"[M+H]+U'+"112.050773620605469,0.042819745838642,1,"MI:C'+"|136.061843872070313,0.196844235062599,1,"MI:A'+"|152.056671142578125,0.023113740608096,1,"MI:G'+"|153.1024169921875,0.012729996815324,1,"a2-C1H4S1+"|158.092819213867188,0.016056764870882,1,"y1-H3N1+"|175.118804931640625,0.146781176328659,1,"y1+"|182.092300415039063,0.052632980048656,1,"a1+U'+"|227.065277099609375,0.01328039355576,1,"MI:U-H3PO4+"|245.076187133789063,0.142766728997231,1,"MI:U-HPO3+"|253.100723266601563,9.467311203479767e-03,1,"a2+C3O+"|281.09564208984375,9.001040831208229e-03,1,"b2+C3O+"|288.20294189453125,8.992226794362068e-03,1,"y2+"|296.12347412109375,0.02242861315608,1,"a1+U-H3PO4+"|313.13702392578125,0.016673086211085,1,"a2+U'+"|341.126983642578125,0.080299213528633,1,"b2+U'+"|348.068084716796875,9.060680866241455e-03,1,"MI:A+"|376.089996337890625,0.029012143611908,1,"a1+U-H2O+"|394.095611572265625,0.040202785283327,1,"a1+U+"|427.164215087890625,0.022860564291477,1,"a2+U-H3PO4+"|525.14324951171875,0.028857138007879,1,"a2+U+"|527.2733154296875,1.0,2,"[M+2H-H2O]++"|535.1282958984375,7.558762095868588e-03,1,"b2+U-H2O+"|553.13372802734375,0.032937977463007,1,"b2+U+"|553.27215576171875,0.012286836281419,1,"NDNIL-H3N1+"|640.3057861328125,0.033281195908785,2,"[M+2H-H2O]+U-H3PO4++"|649.3082275390625,0.248698011040688,2,"[M+2H]+U-H3PO4++"|669.29034423828125,0.01186771504581,1,"MVNDNI-H2O1+"|825.46112060546875,0.037652637809515,1,"y7-H2O1+"|956.483642578125,0.047358602285385,1,"y8-H2O1+"|1053.5389404296875,0.277017205953598,1,"[M+H-H2O]+"|1123.5164794921875,0.02236651070416,1,"b8+U-H3PO4+"|1183.5704345703125,0.054004456847906,1,"[M+H]+U'+" +39.118 623.2540 Cse2 MLTWWGK U 2 48.237815856933594 1 1.08866548538208 0,0.95,0,108.87,16.34,0,7.64 MLTwWGK 920.4578 324.0359 1244.4937 3.611835241317749 2.463027238845825 1 1 1 0 0.372912466526032 0.0 0.215587794780731 2 315.0 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 0.0002 -0.3 1245.5010 623.2541 415.8385 312.1307 112.050796508789063,0.103300340473652,1,"MI:C'+"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'+"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O+"|147.112686157226563,0.124614141881466,1,"y1+"|152.056869506835938,0.015434425324202,1,"MI:G'+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2+"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2+"|245.132080078125,0.17075103521347,1,"b2+"|346.179931640625,0.042745251208544,1,"b3+"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4++"|390.2135009765625,0.532232463359833,1,"y3+"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4+"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4++"|465.1192626953125,0.018610520288348,1,"iW+U-H2O++"|483.1278076171875,0.129291772842407,1,"iW+U++"|789.36456298828125,0.076395474374294,1,"y5+U'+"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4+"|882.31549072265625,0.055004987865686,1,"y4+U-H2O+"|900.32177734375,0.064147591590881,1,"y4+U+"|902.44384765625,0.015058934688568,1,"y6+U'+"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4+"|983.36517333984375,0.134756237268448,1,"y5+U-H2O+"|1001.3760986328125,0.190459117293358,1,"y5+U+"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+U'+"|1096.445556640625,0.048582393676043,1,"y6+U-H2O+"|1114.4610595703125,0.042080584913492,1,"y6+U+" +39.853 861.3889 Cas5 LAGPMQAWGQPTFEGTRPTGR U 3 37.401420593261719 1 2.457196474075317 0,0,0,0,0,0,0,0,244.47,0,0,0,0,0,0,0,0,0,245.72,0,0 LAGPMQAWGQPTFEGTRPtGR 2257.1062 324.0359 2581.1421 9.457996368408203 11.046560287475586 1 1 1 0 0.13300721347332 0.0 0.168000027537346 2 315.0 0 14.94 3.38 3.08 0.00 1.95 0.00 0.00 0.00 -0.0009 1.1 2582.1494 1291.5783 861.3880 646.2928 112.050376892089844,0.03075241483748,1,"MI:C'+"|127.086822509765625,0.084323570132256,1,"GP-CO"|136.061492919921875,0.149392291903496,1,"MI:A'+"|152.056304931640625,0.019498618319631,1,"MI:G'+"|153.101638793945313,0.027191694825888,1,"PM-CO-C1H4S1+"|155.081680297851563,0.129901498556137,1,"GP"|157.1085205078125,0.016523864120245,1,"y1-H2O1+"|157.133346557617188,0.116147078573704,1,"a2+"|158.092391967773438,0.186959013342857,1,"y1-H3N1+"|172.1072998046875,0.019877409562469,1,"QA-CO"|175.118942260742188,0.864344000816345,1,"y1+"|185.128372192382813,0.101255014538765,1,"b2+"|200.10223388671875,0.099220559000969,1,"QA"|226.117660522460938,0.046638753265142,1,"AGP"|228.13330078125,0.014135158620775,1,"PTG-CO"|229.09967041015625,0.03934133425355,1,"PM"|230.129501342773438,9.715269319713116e-03,1,"AW-CO"|232.1397705078125,0.013686842285097,1,"y2+"|242.149429321289063,0.073746532201767,1,"b3+"|260.10400390625,0.014170597307384,1,"MQ"|281.159515380859375,0.051366787403822,1,"AGPM-CO-C1H4S1+"|286.121002197265625,0.049559332430363,1,"GPM"|303.146270751953125,0.076557174324989,3,"b8+C3O+++"|313.1822509765625,8.80386121571064e-03,1,"TRP-C1H2N2+"|315.144927978515625,0.083149679005146,1,"AWG"|329.163055419921875,0.014427128247917,1,"AGPM-CO"|331.139739990234375,0.012301723472774,1,"MQA"|357.157958984375,0.112319760024548,1,"AGPM"|370.20562744140625,0.010619016364217,1,"GTRP-C1H2N2+"|372.708740234375,0.117013581097126,2,"y7++"|386.179534912109375,0.045954059809446,1,"QAW"|394.2432861328125,0.019391525536776,1,"a5-C1H4S1+"|397.153350830078125,0.014580637216568,1,"GPMQ-H3N1+"|414.1788330078125,0.048771116882563,1,"GPMQ"|426.172393798828125,0.011522333137691,1,"AWGQ-H3N1+"|428.194000244140625,0.016342636197805,1,"PMQA"|430.24169921875,0.102167457342148,1,"y4+"|443.201904296875,0.046294238418341,1,"QAWG"|468.190093994140625,0.045015033334494,1,"AGPMQ-H3N1+"|485.219146728515625,0.061722680926323,1,"AGPMQ"|570.2940673828125,0.015357924625278,1,"GTRPTG"|577.2655029296875,0.01251458004117,1,"y3+U-HPO3+"|581.27789306640625,0.01857952028513,1,"b6-H3N1+"|582.268798828125,0.013687066733837,1,"b5+U'+"|598.30841064453125,0.012375350110233,1,"b6+"|609.81640625,0.391953557729721,2,"y11++"|660.29052734375,0.011049717664719,1,"GQPTFE"|665.32275390625,0.049633823335171,2,"y12-H3N1++"|670.325927734375,0.010814912617207,1,"FEGTRP-H2O1+"|671.30474853515625,0.033622957766056,1,"GPMQAW"|673.8443603515625,0.12153934687376,2,"y12++"|699.315185546875,0.014566479250789,1,"GQPTFEG-H2O1+"|702.3807373046875,0.015244751237333,1,"y7-C1H2N2+"|728.35498046875,0.048261545598507,2,"y13+C3O++"|744.40643310546875,0.051093131303787,1,"y7+"|758.361328125,0.14195054769516,2,"y13+U'++"|767.34393310546875,0.093842588365078,3,"y19+U-H3PO4+++"|774.99993896484375,0.047129739075899,3,"y18+U-H2O+++"|781.00018310546875,0.071356788277626,3,"y18+U+++"|782.33447265625,0.026894029229879,1,"AGPMQAWG-H3N1+"|815.3856201171875,0.147706180810928,2,"b13+U-HPO3++"|851.41131591796875,0.183295845985413,2,"y14+U'++"|862.4254150390625,0.215514808893204,1,"TFEGTRPT-CO"|886.9246826171875,0.320382863283157,2,"y15+U'++"|899.40863037109375,0.029477229341865,2,"b15+U-H3PO4++"|908.42529296875,0.371884346008301,2,"y14+U-H3PO4++"|942.45684814453125,0.053394634276628,1,"PTFEGTRPT-CO-H3N1+"|943.94268798828125,0.374551713466644,2,"y15+U-H3PO4++"|951.449951171875,0.069044589996338,2,"y17-H2O1++"|953.4407958984375,0.018099347129464,1,"GPMQAWGQP"|957.4124755859375,0.12921978533268,2,"y14+U++"|983.93023681640625,0.169056877493858,2,"y15+U-H2O++"|992.9346923828125,0.170678496360779,2,"y15+U++"|1000.46746826171875,0.030669666826725,1,"QAWGQPTFE-CO-H3N1+"|1007.9669189453125,0.198151588439941,2,"y16+U-H3PO4++"|1113.4766845703125,0.044029250741005,2,"y17+U-H2O++"|1122.482666015625,0.080889888107777,2,"y17+U++" +40.038 1043.4525 Cas7 SGYYAQNIGESSLRTIHLAQLR GU-H2O1 3 12.18718147277832 1 0.0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 SGYYAQNIGESSLRTIHLAQLR 2476.2823 651.0727 3127.3550 4.506982803344727 0.042108997702599 1 1 1 0 0.193572551012039 0.0 2.997914329171181e-03 1 315.0 0 11.70 1.76 0.00 0.00 0.89 0.00 0.00 0.00 0.0064 -6.2 3128.3623 1564.6848 1043.4590 782.8460 129.066375732421875,0.011452200822532,1,"SS-CO-H2O1+"|136.062057495117188,0.117006808519363,1,"MI:A'+"|136.075942993164063,0.061224263161421,1,"iY+"|147.076553344726563,0.033742658793926,1,"SS-CO"|152.05645751953125,8.929258212447167e-03,1,"MI:G'+"|157.10845947265625,0.019333818927407,1,"y1-H2O1+"|158.092269897460938,0.014068718068302,1,"y1-H3N1+"|175.11895751953125,1.0,1,"y1+"|200.10223388671875,0.037957575172186,1,"AQ"|200.13934326171875,0.015138491056859,1,"NI-CO"|207.112930297851563,0.018860274925828,1,"YA-CO"|227.066238403320313,0.013174916617572,1,"MI:U-H3PO4+"|228.134735107421875,0.140522807836533,1,"NI"|235.107940673828125,0.038548536598682,1,"YA"|242.149642944335938,0.085332110524178,1,"SSL-CO-H2O1+"|258.1038818359375,0.021212872117758,1,"ESS-CO-H2O1+"|271.17724609375,0.036110296845436,1,"y2-H3N1+"|288.20263671875,0.540427029132843,1,"y2+"|313.187530517578125,0.047560345381498,1,"LAQ"|352.200225830078125,0.011090287938714,1,"TIH"|371.19293212890625,0.051817037165165,1,"ESSL-CO-H2O1+"|398.252685546875,0.013688288629055,1,"y3-H2O1+"|399.237579345703125,0.012889615260065,1,"y3-H3N1+"|416.261444091796875,0.611584186553955,1,"y3+"|427.2349853515625,0.017148498445749,1,"AQNI"|428.2210693359375,0.057390972971916,1,"IGESS-CO-H2O1+"|470.27783203125,0.012210931628942,1,"y4-H3N1+"|487.298919677734375,0.575224339962006,1,"y4+"|514.23504638671875,0.032693766057491,1,"a5+"|541.30743408203125,0.047687828540802,1,"IGESSL-CO-H2O1+"|542.22161865234375,0.017067449167371,1,"b5+"|573.2657470703125,0.016528343781829,1,"YAQNI-H3N1+"|596.27105712890625,0.011223017238081,1,"AQNIGE-H3N1+"|613.29095458984375,0.011800601147115,1,"GESSLR-H3N1+"|630.299072265625,0.011752335354686,1,"YAQNIG-H3N1+"|636.37835693359375,0.014756876043975,1,"TIHLAQ-CO"|647.3037109375,0.027322037145495,1,"YAQNIG"|655.31170654296875,0.017578417435288,1,"AQNIGES-CO-H3N1+"|672.33526611328125,0.207145139575005,1,"AQNIGES-CO"|888.46136474609375,0.064613588154316,1,"NIGESSLRT-CO-C1H2N2+"|967.49603271484375,0.044361278414726,1,"QNIGESSLR-H2O1+"|985.50390625,0.146545097231865,1,"QNIGESSLR"|1042.531005859375,0.303900748491287,1,"QNIGESSLRT-C1H2N1O1+"|1221.4688720703125,0.043008159846067,1,"b8+U+" diff --git a/src/tests/topp/OpenNuXL_5_output.idXML b/src/tests/topp/OpenNuXL_5_output.idXML index 734ec280a85..b74046982bd 100644 --- a/src/tests/topp/OpenNuXL_5_output.idXML +++ b/src/tests/topp/OpenNuXL_5_output.idXML @@ -6,7 +6,7 @@ - + @@ -32,7 +32,7 @@ - + @@ -70,7 +70,7 @@ - + @@ -112,7 +112,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -272,7 +272,7 @@ - + @@ -309,8 +309,8 @@ - - + + @@ -352,7 +352,7 @@ - + @@ -389,8 +389,8 @@ - - + + @@ -432,7 +432,7 @@ - + @@ -512,7 +512,7 @@ - + @@ -592,7 +592,7 @@ - + @@ -672,7 +672,7 @@ - + @@ -752,7 +752,7 @@ - + @@ -789,8 +789,8 @@ - - + + @@ -832,7 +832,7 @@ - + @@ -869,8 +869,8 @@ - - + + @@ -912,7 +912,7 @@ - + @@ -949,8 +949,8 @@ - - + + @@ -992,7 +992,7 @@ - + @@ -1072,7 +1072,7 @@ - + @@ -1232,7 +1232,7 @@ - + @@ -1269,8 +1269,8 @@ - - + + @@ -1312,7 +1312,7 @@ - + @@ -1392,7 +1392,7 @@ - + @@ -1472,7 +1472,7 @@ - + @@ -1552,7 +1552,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_6_output.idXML b/src/tests/topp/OpenNuXL_6_output.idXML index fdbbb456e79..2953f8d5e74 100644 --- a/src/tests/topp/OpenNuXL_6_output.idXML +++ b/src/tests/topp/OpenNuXL_6_output.idXML @@ -6,7 +6,7 @@ - + @@ -36,7 +36,7 @@ - + @@ -74,7 +74,7 @@ - + @@ -112,7 +112,7 @@ - + @@ -150,7 +150,7 @@ - + @@ -340,7 +340,7 @@ - + @@ -416,7 +416,7 @@ - + @@ -644,7 +644,7 @@ - + @@ -720,7 +720,7 @@ - + @@ -948,7 +948,7 @@ - + @@ -985,8 +985,8 @@ - - + + @@ -1024,7 +1024,7 @@ - + @@ -1252,7 +1252,7 @@ - + @@ -1289,8 +1289,8 @@ - - + + @@ -1328,7 +1328,7 @@ - + @@ -1365,8 +1365,8 @@ - - + + @@ -1556,7 +1556,7 @@ - + @@ -1632,7 +1632,7 @@ - + @@ -1788,7 +1788,7 @@ - + @@ -1864,7 +1864,7 @@ - + @@ -2088,7 +2088,7 @@ - + @@ -2164,7 +2164,7 @@ - + @@ -2392,7 +2392,7 @@ - + @@ -2468,7 +2468,7 @@ - + @@ -2696,7 +2696,7 @@ - + @@ -2733,8 +2733,8 @@ - - + + @@ -2772,7 +2772,7 @@ - + @@ -2809,8 +2809,8 @@ - - + + @@ -2928,7 +2928,7 @@ - + @@ -2965,8 +2965,8 @@ - - + + @@ -3004,7 +3004,7 @@ - + @@ -3041,8 +3041,8 @@ - - + + @@ -3312,7 +3312,7 @@ - + @@ -3349,8 +3349,8 @@ - - + + @@ -3540,7 +3540,7 @@ - + @@ -3616,7 +3616,7 @@ - + @@ -3848,7 +3848,7 @@ - + @@ -3924,7 +3924,7 @@ - + @@ -4460,7 +4460,7 @@ - + @@ -4497,8 +4497,8 @@ - - + + @@ -4536,7 +4536,7 @@ - + @@ -4573,8 +4573,8 @@ - - + + @@ -4764,7 +4764,7 @@ - + @@ -4840,7 +4840,7 @@ - + @@ -5068,7 +5068,7 @@ - + @@ -5144,7 +5144,7 @@ - + @@ -5372,7 +5372,7 @@ - + @@ -5448,7 +5448,7 @@ - + @@ -5680,7 +5680,7 @@ - + @@ -5756,7 +5756,7 @@ - + diff --git a/src/tests/topp/OpenNuXL_6_output2.tsv b/src/tests/topp/OpenNuXL_6_output2.tsv index 25cec195212..5d50c826e97 100644 --- a/src/tests/topp/OpenNuXL_6_output2.tsv +++ b/src/tests/topp/OpenNuXL_6_output2.tsv @@ -1,81 +1,81 @@ #RT m/z proteins peptide NA charge score rank best localization score localization scores best localization(s) peptide weight NA weight cross-link weight NuXL:total_loss_score NuXL:partial_loss_score CountSequenceIsTop CountSequenceCharges CountSequenceIsXL CountSequenceIsPeptide NuXL:MIC NuXL:pl_pc_MIC NuXL:pl_MIC nr_candidates -ln(poisson) isotope_error A_136.062309999999997 A_330.060330000000022 C_112.051079999999999 C_306.04910000000001 G_152.057230000000004 G_346.055250000000001 U_113.035089999999997 U_307.033110000000022 abs prec. error Da rel. prec. error ppm M+H M+2H M+3H M+4H fragment_annotation -17.788 712.7828 Cas7 AEADNLDDKK U-H3O4P1 2 66.026290893554688 1 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 226.0590 1343.5841 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 55.851314362896943 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -39.9835 59428.6 1344.5914 672.7993 448.8686 336.9033 112.050621032714844,0.028104400262237,1,"MI:C'+"|129.102218627929688,0.026284486055374,1,"y1-H2O1+"|130.086135864257813,0.027207279577851,1,"y1-H3N1+"|136.061904907226563,0.044882696121931,1,"MI:A'+"|141.065628051757813,0.054898034781218,1,"AD-CO-H2O1+"|147.112884521484375,0.075572468340397,1,"y1+"|155.081436157226563,0.136838972568512,1,"a2-H2O1+"|159.076019287109375,0.029015546664596,1,"AD-CO"|173.091934204101563,0.683034300804138,1,"a2+"|178.097335815429688,0.089906625449657,1,"iK(C5H10N1)U'-H2O+"|183.076751708984375,0.023124447092414,1,"b2-H2O1+"|187.0716552734375,0.051760952919722,1,"AD"|200.139236450195313,0.022941825911403,1,"NL-CO"|201.0867919921875,1.0,1,"b2+"|228.1337890625,0.024709410965443,1,"NL"|230.077316284179688,0.050377540290356,1,"DN"|244.129180908203125,6.143126636743546e-03,1,"a3+"|254.11285400390625,6.038205698132515e-03,1,"b3-H2O1+"|256.09375,6.242495961487293e-03,1,"ADN-CO-H3N1+"|270.108612060546875,7.826141081750393e-03,1,"EAD-CO-H2O1+"|272.1239013671875,0.143406257033348,1,"b3+"|283.102874755859375,7.825194858014584e-03,1,"ADN-H2O1+"|284.08636474609375,6.175518501549959e-03,1,"ADN-H3N1+"|298.104034423828125,0.042165260761976,1,"EAD-H2O1+"|298.137481689453125,7.229866925626993e-03,1,"LDD-CO-H2O1+"|301.11376953125,0.105918377637863,1,"ADN"|316.11285400390625,0.030915109440684,1,"EAD"|338.1446533203125,0.022856334224343,1,"a3+U'-H2O+"|341.14337158203125,5.692003294825554e-03,1,"a4-H2O1+"|343.158599853515625,6.486350204795599e-03,1,"DNL"|356.154693603515625,5.492141470313072e-03,1,"a3+U'+"|369.13873291015625,0.015835056081414,1,"b4-H2O1+"|369.179473876953125,0.015010283328593,1,"ADNL-CO-H3N1+"|369.2237548828125,0.374819993972778,1,"y2+U'-H2O+"|384.151763916015625,6.279260385781527e-03,1,"EADN-CO-H2O1+"|386.20269775390625,0.031310774385929,1,"ADNL-CO"|387.150390625,0.08102560788393,1,"b4+"|397.170989990234375,7.334685418754816e-03,1,"ADNL-H3N1+"|412.186187744140625,0.011006367392838,1,"DNLD-CO-H2O1+"|413.1322021484375,0.022974291816354,1,"EADN-H3N1+"|413.70587158203125,0.121404588222504,2,"y6+U'-H2O++"|430.15765380859375,0.011116344481707,1,"EADN"|438.163909912109375,8.430351503193378e-03,1,"LDD+U'-H2O+"|453.1707763671875,0.05518963560462,1,"a4+U'-H2O+"|454.18902587890625,7.05699622631073e-03,1,"NL+U-H3PO4+"|456.17205810546875,0.037782747298479,1,"a5-H3N1+"|471.22369384765625,0.088998980820179,2,"y7+U'-H2O++"|483.1859130859375,0.011534767225385,1,"b5-H2O1+"|484.167816162109375,0.101781167089939,1,"b5-H3N1+"|484.25115966796875,0.309119403362274,1,"y3+U'-H2O+"|501.19091796875,0.035030111670494,1,"b5+"|506.737823486328125,0.32832595705986,2,"y8+U'-H2O++"|508.205657958984375,6.574578117579222e-03,1,"ADNL+U'-H2O+"|525.2352294921875,7.42009561508894e-03,1,"EADNL-H2O1+"|526.21826171875,6.489385850727558e-03,1,"EADNL-H3N1+"|529.2286376953125,6.844865623861551e-03,1,"ADNLD"|543.24212646484375,8.318453095853329e-03,1,"EADNL"|566.25738525390625,0.027678105980158,1,"LDDK+U'-H2O+"|569.2574462890625,0.030402790755033,1,"a6-H3N1+"|571.2596435546875,0.054311472922564,2,"y9+U'-H2O++"|584.267578125,9.894491173326969e-03,1,"LDDK+U'+"|586.28167724609375,0.011093857698143,1,"a6+"|597.24884033203125,0.025496212765574,1,"b6-H3N1+"|597.773681640625,0.176505729556084,2,"[M+2H-H2O]+U'-H2O++"|599.27777099609375,0.764611601829529,1,"y4+U'-H2O+"|606.77734375,0.299497008323669,2,"[M+2H]+U'-H2O++"|614.27984619140625,0.039939478039742,1,"b6+"|680.2978515625,0.018134105950594,1,"a6+U'-H2O+"|698.31036376953125,6.59028347581625e-03,1,"LDDK+U-H3PO4+"|712.36236572265625,0.394213527441025,1,"y5+U'-H2O+"|729.31292724609375,6.610926240682602e-03,1,"b7+"|795.32373046875,0.023242574185133,1,"a7+U'-H2O+"|826.40509033203125,0.400069534778595,1,"y6+U'-H2O+"|844.32489013671875,6.451499182730913e-03,1,"b8+"|866.3614501953125,0.062791705131531,1,"ADNLDDK+U'-H2O+"|884.37408447265625,7.893706671893597e-03,1,"EADNLDDK-H3N1+"|941.43206787109375,0.44364058971405,1,"y7+U'-H2O+"|1012.468994140625,0.708723366260529,1,"y8+U'-H2O+"|1066.4478759765625,0.035385373979807,1,"b9+U'-H2O+"|1141.5120849609375,7.319674827158451e-03,1,"y9+U'-H2O+"|1212.5546875,0.066727869212627,1,"[M+H]+U'-H2O+" -17.788 712.7828 Cas7 AEADNLDDKK U-H2O1 2 65.480873107910156 2 4.120850563049316 0,0,16.03,13.20,0,7.68,5.86,0,412.09,8.99 AEADNLDDkK 1117.5251 306.0253 1423.5504 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 55.851314362896943 0 11.444543838500977 15.996561050415039 1 1 1 0 0.216474175453186 3.056259393692017 0.370656102895737 29253 55.851314362896943 0 4.49 0.00 2.81 0.00 0.00 0.00 0.00 0.00 -0.0003 0.5 1424.5577 712.7825 475.5241 356.8949 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-18.306 590.7661 Cas6e DLYQLHQGLWHLFPNR none 2 8.358111381530762 4 0.0 0 DLYQLHQGLWHLFPNR 2036.0381 0.0000 2036.0381 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.778190140393486 0 0.948040783405304 0.0 0.042552266269922 0.0 0.0 29253 5.328151996774687 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 428.2603 -420264.2 2037.0453 1019.0263 679.6866 510.0168 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-25.116 508.1855 Cas5 YTPYLGR U-H3O4P1 3 30.759143829345703 1 0.637990474700928 0,0.24,0,63.80,0,0,0 YTPyLGR 868.4443 226.0590 1094.5033 3.710045576095581 2.12938380241394 1 1 1 0 0.190965637564659 2.006152153015137 0.109201602637768 29253 24.764919939353597 0 100.00 3.85 0.00 0.00 0.43 0.00 0.00 0.00 -142.3438 389085.8 1095.5106 548.2589 365.8417 274.6331 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112.051109313964844,0.062729187309742,1,"MI:C'+"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'+"|147.112808227539063,0.358728766441345,1,"y1+"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O+"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2+"|229.117584228515625,0.131456702947617,1,"b2+"|260.1971435546875,0.07334553450346,1,"y2+"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O++"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O++"|431.26043701171875,0.208169266581535,1,"y4+"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]+U'-H2O++"|484.760772705078125,1.0,2,"[M+2H-H2O]+U'++"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]+U-H3PO4++"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O+"|653.369873046875,0.024192033335567,1,"y5+U'-H2O+"|709.32696533203125,0.225882858037949,1,"b6+U'-H2O+"|740.40380859375,0.319797694683075,1,"y6+U'-H2O+"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O+"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O+"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O+" +18.306 590.7661 Cas6e LDSKGNIK U-H2O1 2 31.744165420532227 2 2.196093797683716 0,0,0,219.61,0,0,0,8.00 LDSkGNIK 873.4920 306.0253 1179.5173 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -0.0001 0.2 1180.5246 590.7659 394.1797 295.8866 112.051109313964844,0.062729187309742,1,"MI:C'+"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'+"|147.112808227539063,0.358728766441345,1,"y1+"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O+"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2+"|229.117584228515625,0.131456702947617,1,"b2+"|260.1971435546875,0.07334553450346,1,"y2+"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O++"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O++"|431.26043701171875,0.208169266581535,1,"y4+"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]+U'-H2O++"|484.760772705078125,1.0,2,"[M+2H-H2O]+U'++"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]+U-H3PO4++"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O+"|653.369873046875,0.024192033335567,1,"y5+U'-H2O+"|709.32696533203125,0.225882858037949,1,"b6+U'-H2O+"|740.40380859375,0.319797694683075,1,"y6+U'-H2O+"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O+"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O+"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O+"112.051109313964844,0.062729187309742,1,"MI:C'+"|129.10223388671875,0.266797989606857,1,"y1-H2O1+"|130.08636474609375,0.182156324386597,1,"y1-H3N1+"|136.061492919921875,0.177392527461052,1,"MI:A'+"|147.112808227539063,0.358728766441345,1,"y1+"|178.097763061523438,0.079973883926868,1,"iK(C5H10N1)U'-H2O+"|183.112701416015625,0.06690613925457,1,"a2-H2O1+"|201.12353515625,0.118377678096294,1,"a2+"|229.117584228515625,0.131456702947617,1,"b2+"|260.1971435546875,0.07334553450346,1,"y2+"|370.705230712890625,0.899306416511536,2,"y6+U'-H2O++"|428.219207763671875,0.510025024414063,2,"y7+U'-H2O++"|431.26043701171875,0.208169266581535,1,"y4+"|475.756744384765625,0.235214054584503,2,"[M+2H-H2O]+U'-H2O++"|484.760772705078125,1.0,2,"[M+2H-H2O]+U'++"|541.77874755859375,0.097188904881477,2,"[M+2H-H2O]+U-H3PO4++"|595.28948974609375,0.030613591894507,1,"b5+U'-H2O+"|653.369873046875,0.024192033335567,1,"y5+U'-H2O+"|709.32696533203125,0.225882858037949,1,"b6+U'-H2O+"|740.40380859375,0.319797694683075,1,"y6+U'-H2O+"|794.41949462890625,0.029359607025981,1,"a7+U'-H2O+"|822.41180419921875,0.126908898353577,1,"b7+U'-H2O+"|855.42803955078125,0.362798720598221,1,"y7+U'-H2O+" +18.306 590.7661 Cas6e LDSKGNIK none 2 12.331851959228516 3 0.0 0 LDSKGNIK 873.4920 0.0000 873.4920 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.778190140393486 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 -153.0128 349541.2 874.4993 437.7533 292.1713 219.3803 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+18.306 590.7661 Cas6e DLYQLHQGLWHLFPNR none 2 8.358111381530762 4 0.0 0 DLYQLHQGLWHLFPNR 2036.0381 0.0000 2036.0381 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 4.334724426269531 1 1 1 0 0.130456954240799 3.195287704467773 0.164090722799301 29253 26.087011578114502 0 2.428377628326416 0.0 1 1 1 0 0.130456954240799 0.0 0.0 29253 7.778190140393486 0 0.948040783405304 0.0 0.042552266269922 0.0 0.0 29253 5.328151996774687 0 17.74 0.00 6.27 0.00 0.00 0.00 0.00 0.00 428.2603 -420264.2 2037.0453 1019.0263 679.6866 510.0168 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-34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK UU-H2O1 2 31.977167129516602 2 0.686758100986481 0,0,0,68.68,0,0,0,0,6.09 MVFcLSAGK 970.4616 612.0506 1582.5122 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 144.0075 -181767.2 1583.5195 792.2634 528.5114 396.6353 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-34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK none 2 21.468671798706055 3 0.0 0 MVFCLSAGK 970.4616 0.0000 970.4616 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 7.007274678147403 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -162.0178 333206.8 971.4689 486.2381 324.4945 243.6227 112.050895690917969,0.209176629781723,1,"MI:C'+"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'+"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O+"|147.112640380859375,0.216315641999245,1,"y1+"|152.056716918945313,0.298746705055237,1,"MI:G'+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+"|630.2962646484375,0.098198756575584,1,"y6+C3O+"|690.31988525390625,0.040793959051371,1,"y6+U'+"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4+"|837.3975830078125,0.075952410697937,1,"y7+U'+"|884.31402587890625,0.01827629096806,1,"y6+U-H2O+"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4+"|1031.390869140625,0.102401345968246,1,"y7+U-H2O+"112.050895690917969,0.209176629781723,1,"MI:C'+"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'+"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O+"|147.112640380859375,0.216315641999245,1,"y1+"|152.056716918945313,0.298746705055237,1,"MI:G'+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+"|630.2962646484375,0.098198756575584,1,"y6+C3O+"|688.197998046875,0.013070179149508,1,"FCL+U+"|690.31988525390625,0.040793959051371,1,"y6+U'+"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4+"|837.3975830078125,0.075952410697937,1,"VFCLSA-CO+U-HPO3+"|884.31402587890625,0.01827629096806,1,"y6+U-H2O+"|902.33062744140625,0.050201874226332,1,"y6+U+"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4+"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3+"|1031.390869140625,0.102401345968246,1,"y7+U-H2O+"|1049.4049072265625,0.163576155900955,1,"y7+U+"120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|147.112640380859375,0.216315641999245,1,"y1+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+" -34.072 648.2559 Cse2 HQQALLRMVFCLSAGK none 2 16.85017204284668 4 0.0 0 HQQALLRMVFCLSAGK 1800.9491 0.0000 1800.9491 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 7.007274678147403 0 5.535978317260742 0.0 0.133406266570091 0.0 0.0 29253 5.499638206201645 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 253.2259 -280899.6 1801.9564 901.4818 601.3237 451.2446 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+34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK UU-H2O1 2 31.977167129516602 2 0.762710511684418 0,0,0,76.27,0,0,0,0,6.09 MVFcLSAGK 970.4616 612.0506 1582.5122 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 144.0075 -181767.2 1583.5195 792.2634 528.5114 396.6353 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+34.072 648.2559 Cse2 M(Oxidation)VFCLSAGK none 2 21.468671798706055 3 0.0 0 MVFCLSAGK 970.4616 0.0000 970.4616 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 1.056356310844421 1 1 1 0 0.223560705780983 0.0 0.052454251796007 29253 10.407393442944352 0 6.533727645874023 0.0 1 1 1 0 0.223560705780983 0.0 0.0 29253 7.007274678147403 0 100.00 18.53 20.92 0.00 29.87 0.00 0.00 2.08 -162.0178 333206.8 971.4689 486.2381 324.4945 243.6227 112.050895690917969,0.209176629781723,1,"MI:C'+"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'+"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O+"|147.112640380859375,0.216315641999245,1,"y1+"|152.056716918945313,0.298746705055237,1,"MI:G'+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+"|630.2962646484375,0.098198756575584,1,"y6+C3O+"|690.31988525390625,0.040793959051371,1,"y6+U'+"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4+"|837.3975830078125,0.075952410697937,1,"y7+U'+"|884.31402587890625,0.01827629096806,1,"y6+U-H2O+"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4+"|1031.390869140625,0.102401345968246,1,"y7+U-H2O+"112.050895690917969,0.209176629781723,1,"MI:C'+"|120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|136.061874389648438,1.0,1,"MI:A'+"|136.074905395507813,0.060894824564457,1,"iK(C5H10N1)C3O+"|147.112640380859375,0.216315641999245,1,"y1+"|152.056716918945313,0.298746705055237,1,"MI:G'+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|307.0333251953125,0.020802663639188,1,"MI:U-H2O+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|348.070465087890625,0.068254500627518,1,"MI:A+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+"|630.2962646484375,0.098198756575584,1,"y6+C3O+"|690.31988525390625,0.040793959051371,1,"y6+U'+"|804.358642578125,0.037921737879515,1,"y6+U-H3PO4+"|837.3975830078125,0.075952410697937,1,"y7+U'+"|884.31402587890625,0.01827629096806,1,"y6+U-H2O+"|902.33062744140625,0.050201874226332,1,"y6+U+"|951.42193603515625,0.162590846419334,1,"y7+U-H3PO4+"|969.44110107421875,0.012797155417502,1,"y7+U-HPO3+"|1031.390869140625,0.102401345968246,1,"y7+U-H2O+"|1049.4049072265625,0.163576155900955,1,"y7+U+"120.08087158203125,0.124347224831581,1,"iF+"|129.10235595703125,0.228462561964989,1,"y1-H2O1+"|130.031997680664063,0.035823903977871,1,"b1-H2O1+"|130.086135864257813,0.118066854774952,1,"y1-H3N1+"|147.112640380859375,0.216315641999245,1,"y1+"|155.118011474609375,0.20624178647995,1,"a2-C1H4O1S1+"|183.113006591796875,0.021374877542257,1,"b2-C1H4O1S1+"|186.123565673828125,0.06671004742384,1,"y2-H2O1+"|187.107284545898438,0.014260332100093,1,"y2-H3N1+"|204.134185791015625,0.293448150157928,1,"y2+"|219.116134643554688,0.69442480802536,1,"a2+"|247.111434936523438,0.152931392192841,1,"b2+"|258.14532470703125,0.017768338322639,1,"y3-H3N1+"|275.170379638671875,0.12989653646946,1,"y3+"|302.18646240234375,0.010382685810328,1,"a3-C1H4O1S1+"|330.1796875,0.019829308614135,1,"b3-C1H4O1S1+"|362.202789306640625,0.197416797280312,1,"y4+"|394.17913818359375,0.058901127427816,1,"b3+"|475.288665771484375,0.123156972229481,1,"y5+" 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112.050796508789063,0.103300340473652,1,"MI:C'+"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'+"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O+"|147.112686157226563,0.124614141881466,1,"y1+"|152.056869506835938,0.015434425324202,1,"MI:G'+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2+"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2+"|245.132080078125,0.17075103521347,1,"b2+"|346.179931640625,0.042745251208544,1,"b3+"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4++"|390.2135009765625,0.532232463359833,1,"y3+"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4+"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4++"|457.197662353515625,0.010401514358819,1,"WW-CO+U'+"|465.1192626953125,0.018610520288348,1,"iW+U-H2O++"|483.1278076171875,0.129291772842407,1,"iW+U++"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4+"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4+"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O+"|584.17132568359375,0.068149335682392,1,"TW-CO+U+"|594.158447265625,0.032711785286665,1,"TW+U-H2O+"|612.1688232421875,0.057017870247364,1,"TW+U+"|669.20440673828125,0.012318334542215,1,"WW-CO+U+"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4+"|789.36456298828125,0.076395474374294,1,"y5+U'+"|798.2451171875,0.01280861068517,1,"TWW+U+"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4+"|882.31549072265625,0.055004987865686,1,"y4+U-H2O+"|900.32177734375,0.064147591590881,1,"y4+U+"|902.44384765625,0.015058934688568,1,"y6+U'+"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4+"|983.36517333984375,0.134756237268448,1,"y5+U-H2O+"|1001.3760986328125,0.190459117293358,1,"y5+U+"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+U'+"|1096.445556640625,0.048582393676043,1,"y6+U-H2O+"|1114.4610595703125,0.042080584913492,1,"y6+U+"112.050796508789063,0.103300340473652,1,"MI:C'+"|129.102279663085938,0.140630826354027,1,"y1-H2O1+"|130.08660888671875,0.066025622189045,1,"y1-H3N1+"|136.0618896484375,0.12305948138237,1,"MI:A'+"|136.075668334960938,0.076431922614574,1,"iK(C5H10N1)C3O+"|147.112686157226563,0.124614141881466,1,"y1+"|152.056869506835938,0.015434425324202,1,"MI:G'+"|159.091629028320313,0.047551032155752,1,"iW+"|169.133407592773438,0.017561361193657,1,"a2-C1H4S1+"|187.108078002929688,9.511189535260201e-03,1,"y2-H3N1+"|197.129074096679688,0.016815194860101,1,"b2-C1H4S1+"|204.134078979492188,0.215819895267487,1,"y2+"|215.139007568359375,0.030414596199989,1,"LT"|217.136886596679688,1.0,1,"a2+"|245.132080078125,0.17075103521347,1,"b2+"|346.179931640625,0.042745251208544,1,"b3+"|372.20587158203125,0.014493827708066,1,"y3-H2O1+"|373.18524169921875,0.016838824376464,1,"y3-H3N1+"|385.1505126953125,0.015492090024054,1,"iW+U-H3PO4++"|390.2135009765625,0.532232463359833,1,"y3+"|443.19512939453125,9.507809765636921e-03,1,"a2+U-H3PO4+"|452.211029052734375,0.023706905543804,2,"y5+U-H3PO4++"|457.197662353515625,0.010401514358819,1,"WW-CO+U'+"|465.1192626953125,0.018610520288348,1,"iW+U-H2O++"|483.1278076171875,0.129291772842407,1,"iW+U++"|486.20086669921875,0.013832498341799,1,"TW-CO+U-H3PO4+"|514.1910400390625,0.056320887058973,1,"TW+U-H3PO4+"|566.16131591796875,0.011106071993709,1,"TW-CO+U-H2O+"|584.17132568359375,0.068149335682392,1,"TW-CO+U+"|594.158447265625,0.032711785286665,1,"TW+U-H2O+"|612.1688232421875,0.057017870247364,1,"TW+U+"|669.20440673828125,0.012318334542215,1,"WW-CO+U+"|700.26837158203125,0.010374985635281,1,"TWW+U-H3PO4+"|789.36456298828125,0.076395474374294,1,"y5+U'+"|798.2451171875,0.01280861068517,1,"TWW+U+"|802.360107421875,0.069548688828945,1,"y4+U-H3PO4+"|882.31549072265625,0.055004987865686,1,"y4+U-H2O+"|900.32177734375,0.064147591590881,1,"y4+U+"|902.44384765625,0.015058934688568,1,"y6+U'+"|903.39990234375,0.205530166625977,1,"y5+U-H3PO4+"|983.36517333984375,0.134756237268448,1,"y5+U-H2O+"|1001.3760986328125,0.190459117293358,1,"y5+U+"|1016.48065185546875,0.055152025073767,1,"[M+H-NH3]+U'+"|1096.445556640625,0.048582393676043,1,"y6+U-H2O+"|1114.4610595703125,0.042080584913492,1,"y6+U+" -39.118 623.2540 Cas6e VPLIKEAEQIAWLQR none 2 17.291851043701172 3 0.0 0 VPLIKEAEQIAWLQR 1793.0200 0.0000 1793.0200 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 4.992705345153809 0.0 0.040718141943216 0.0 0.0 29253 8.25391312848474 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 274.2633 -305580.0 1794.0272 897.5173 598.6806 449.2623 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+39.118 623.2540 Cas6e VPLIKEAEQIAWLQR none 2 17.291851043701172 3 0.0 0 VPLIKEAEQIAWLQR 1793.0200 0.0000 1793.0200 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 4.992705345153809 0.0 0.040718141943216 0.0 0.0 29253 8.25391312848474 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 274.2633 -305580.0 1794.0272 897.5173 598.6806 449.2623 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+39.118 623.2540 Cse2 MLTWWGK none 2 17.241123199462891 4 0.0 0 MLTWWGK 920.4578 0.0000 920.4578 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 3.611835241317749 2.420245170593262 1 1 1 0 0.372912466526032 0.0 0.156369626522064 29253 12.545731905702558 0 4.992705345153809 0.0 0.040718141943216 0.0 0.0 29253 8.25391312848474 0 3.611835241317749 0.0 1 1 1 0 0.372912466526032 0.0 0.0 29253 6.328920116015349 0 12.31 1.43 10.33 0.00 1.54 0.00 0.00 0.00 -162.0178 351268.5 921.4651 461.2362 307.8266 231.1217 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From 51ade5b34c2a61203f3a95be7b4ea7915c83cf81 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 23 Jan 2025 16:22:44 +0100 Subject: [PATCH 327/471] increase determinism --- src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp | 1 + src/tests/topp/CMakeLists.txt | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp index 646c1251b61..1474e5a0116 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp @@ -373,6 +373,7 @@ namespace OpenMS // align spectra (only allow matching charges) DataArrays::FloatDataArray ppm_error_array; // not needed here but filled by alignment + removeDuplicatedPeaks(total_loss_spectrum); // remove duplicate peaks based on m/z OPXLSpectrumProcessingAlgorithms::getSpectrumAlignmentFastCharge(alignment, fragment_mass_tolerance, fragment_mass_tolerance_unit_ppm, diff --git a/src/tests/topp/CMakeLists.txt b/src/tests/topp/CMakeLists.txt index 4601faa306d..6ad78d8ef6d 100644 --- a/src/tests/topp/CMakeLists.txt +++ b/src/tests/topp/CMakeLists.txt @@ -1901,7 +1901,7 @@ set_tests_properties("TOPP_OpenNuXL_2_out1" PROPERTIES DEPENDS "TOPP_OpenNuXL_2" # reporting of multiple hits and tsv output add_test("TOPP_OpenNuXL_3" ${TOPP_BIN_PATH}/OpenNuXL -test -precursor:mass_tolerance 10.0 -in -${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_3_output.tmp.idXML -report:top_hits 3 -out_tsv OpenNuXL_3_output2.tmp.tsv -precursor:mass_tolerance 10 -NuXL:scoring fast) +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_3_output.tmp.idXML -report:top_hits 3 -out_tsv OpenNuXL_3_output2.tmp.tsv -NuXL:scoring fast) add_test("TOPP_OpenNuXL_3_out1" ${DIFF} -whitelist "IdentificationRun date" "db=" -in1 OpenNuXL_3_output.tmp.idXML -in2 ${DATA_DIR_TOPP}/OpenNuXL_3_output.idXML ) add_test("TOPP_OpenNuXL_3_out2" ${DIFF} -in1 OpenNuXL_3_output2.tmp.tsv -in2 ${DATA_DIR_TOPP}/OpenNuXL_3_output2.tsv ) @@ -1910,7 +1910,7 @@ set_tests_properties("TOPP_OpenNuXL_3_out2" PROPERTIES DEPENDS "TOPP_OpenNuXL_3" # reporting of multiple hits and tsv output and decoy generation add_test("TOPP_OpenNuXL_4" ${TOPP_BIN_PATH}/OpenNuXL -test -precursor:mass_tolerance 10.0 -in -${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -NuXL:decoys "true" -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_4_output.tmp.idXML -report:top_hits 2 -out_tsv OpenNuXL_4_output2.tmp.tsv -precursor:mass_tolerance 10 -NuXL:scoring fast) +${DATA_DIR_TOPP}/OpenNuXL_1_input.mzML -NuXL:decoys "true" -database ${DATA_DIR_TOPP}/OpenNuXL_1_input.fasta -out OpenNuXL_4_output.tmp.idXML -report:top_hits 2 -out_tsv OpenNuXL_4_output2.tmp.tsv -NuXL:scoring fast) add_test("TOPP_OpenNuXL_4_out1" ${DIFF} -whitelist "IdentificationRun date" "db=" -in1 OpenNuXL_4_output.tmp.idXML -in2 ${DATA_DIR_TOPP}/OpenNuXL_4_output.idXML ) add_test("TOPP_OpenNuXL_4_out2" ${DIFF} -in1 OpenNuXL_4_output2.tmp.tsv -in2 ${DATA_DIR_TOPP}/OpenNuXL_4_output2.tsv ) From 74deac8a813694df175bd89a674b606fc7e756d8 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 23 Jan 2025 19:13:49 +0100 Subject: [PATCH 328/471] stupid windows --- src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp index 1474e5a0116..f14cf4e42f6 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp @@ -425,7 +425,10 @@ namespace OpenMS OPENMS_POSTCONDITION(nt_to_adducts != feasible_MS2_adducts.end(), "Nucleotide not found in mapping to feasible adducts.") - const vector& partial_loss_modification = nt_to_adducts->second; + vector partial_loss_modification = nt_to_adducts->second; + + // TODO: check if needed for reproduciblity + std::stable_sort(partial_loss_modification.begin(), partial_loss_modification.end()); // get marker ions (these are not specific to the cross-linked nucleotide but also depend on the whole oligo bound to the precursor) const vector& marker_ions = all_feasible_adducts.at(precursor_na_adduct).marker_ions; @@ -444,8 +447,11 @@ namespace OpenMS partial_loss_template_z3; partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z1, fixed_and_variable_modified_peptide, 1, 1); + partial_loss_template_z1.sortByPosition(); // need to resort after adding special immonium ions partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z2, fixed_and_variable_modified_peptide, 2, 2); + partial_loss_template_z2.sortByPosition(); // need to resort after adding special immonium ions partial_loss_spectrum_generator.getSpectrum(partial_loss_template_z3, fixed_and_variable_modified_peptide, 3, 3); + partial_loss_template_z3.sortByPosition(); // need to resort after adding special immonium ions NuXLFragmentIonGenerator::generatePartialLossSpectrum(unmodified_sequence, fixed_and_variable_modified_peptide_weight, precursor_na_adduct, From 0177dcd42ad31aac9a4dc661fa18598db7e60761 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Fri, 24 Jan 2025 12:45:56 +0100 Subject: [PATCH 329/471] add tests and documentation for deterministic fragment adduct generation --- .../class_tests/openms/executables.cmake | 1 + .../source/NuXLParameterParsing_test.cpp | 509 ++++++++++++++++++ src/topp/OpenNuXL.cpp | 1 + 3 files changed, 511 insertions(+) create mode 100644 src/tests/class_tests/openms/source/NuXLParameterParsing_test.cpp diff --git a/src/tests/class_tests/openms/executables.cmake b/src/tests/class_tests/openms/executables.cmake index 89dd3844de9..f069f01fedb 100644 --- a/src/tests/class_tests/openms/executables.cmake +++ b/src/tests/class_tests/openms/executables.cmake @@ -519,6 +519,7 @@ set(analysis_executables_list QTClusterFinder_test ReactionMonitoringTransition_test NuXLModificationsGenerator_test + NuXLParameterParsing_test SimpleSearchEngineAlgorithm_test SimpleSVM_test StablePairFinder_test diff --git a/src/tests/class_tests/openms/source/NuXLParameterParsing_test.cpp b/src/tests/class_tests/openms/source/NuXLParameterParsing_test.cpp new file mode 100644 index 00000000000..815bd72c18f --- /dev/null +++ b/src/tests/class_tests/openms/source/NuXLParameterParsing_test.cpp @@ -0,0 +1,509 @@ +// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin +// SPDX-License-Identifier: BSD-3-Clause +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg$ +// $Authors: Timo Sachsenberg$ +// -------------------------------------------------------------------------- + +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +using namespace std; + +/////////////////////////// + +#include +#include + +using namespace OpenMS; +using namespace std; + +START_TEST(NuXLParameterParsing, "$Id$") + +///////////////////////////////////////////////////////////// + +NuXLParameterParsing* ptr = nullptr; +NuXLParameterParsing* nullPointer = nullptr; + +START_SECTION(NuXLParameterParsing()) + ptr = new NuXLParameterParsing(); + TEST_NOT_EQUAL(ptr, nullPointer) +END_SECTION + +START_SECTION(~NuXLParameterParsing()) + delete ptr; +END_SECTION + +START_SECTION((static std::vector getModifications(StringList modNames))) +{ + StringList mods; + mods.push_back("Phospho (S)"); + mods.push_back("Oxidation (M)"); + mods.push_back("Acetyl (N-term)"); + + vector result = NuXLParameterParsing::getModifications(mods); + TEST_EQUAL(result.size(), 3) + TEST_EQUAL(result[0].getId(), "Phospho") + TEST_EQUAL(result[1].getId(), "Oxidation") + TEST_EQUAL(result[2].getId(), "Acetyl") + TEST_EQUAL(result[2].getTermSpecificity(), ResidueModification::N_TERM) +} +END_SECTION + +/* +START_SECTION((static NucleotideToFragmentAdductMap getTargetNucleotideToFragmentAdducts(StringList fragment_adducts))) +{ + StringList fragment_adducts; + fragment_adducts.push_back("U:H-2O-1;U-H2O"); // Format is nucleotide:formula;name + fragment_adducts.push_back("U:H-3P-1O-4;U-H3PO4"); + + NuXLParameterParsing::NucleotideToFragmentAdductMap result = + NuXLParameterParsing::getTargetNucleotideToFragmentAdducts(fragment_adducts); + + TEST_EQUAL(result.size(), 1) // Only U nucleotide + TEST_EQUAL(result['U'].size(), 2) // Two adducts for U + + // Test invalid format + StringList invalid_adducts; + invalid_adducts.push_back("Invalid format"); + NuXLParameterParsing::NucleotideToFragmentAdductMap empty_result = + NuXLParameterParsing::getTargetNucleotideToFragmentAdducts(invalid_adducts); + TEST_EQUAL(empty_result.empty(), true) +} +END_SECTION + +START_SECTION((static MS2AdductsOfSinglePrecursorAdduct getFeasibleFragmentAdducts(const String& exp_pc_adduct, const String& exp_pc_formula, const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, const std::set& can_xl, const bool always_add_default_marker_ions, const bool default_marker_ions_RNA))) +{ + // Create test data + StringList fragment_adducts; + fragment_adducts.push_back("U:H-2O-1;U-H2O"); + NuXLParameterParsing::NucleotideToFragmentAdductMap nuc_to_frag = + NuXLParameterParsing::getTargetNucleotideToFragmentAdducts(fragment_adducts); + + set can_xl = {'U'}; + + // Test monomer case + MS2AdductsOfSinglePrecursorAdduct result = + NuXLParameterParsing::getFeasibleFragmentAdducts( + "U-H2O", // precursor adduct + "C9H11N2O7P", // precursor formula + nuc_to_frag, + can_xl, + true, + true); + + TEST_EQUAL(result.feasible_adducts.size(), 1) // One nucleotide + TEST_NOT_EQUAL(result.marker_ions.size(), 0) // Should have marker ions + + // Test empty precursor formula + MS2AdductsOfSinglePrecursorAdduct empty_result = + NuXLParameterParsing::getFeasibleFragmentAdducts( + "U-H2O", + "", + nuc_to_frag, + can_xl, + true, + true); + + TEST_EQUAL(empty_result.feasible_adducts.empty(), true) + TEST_EQUAL(empty_result.marker_ions.empty(), true) +} +END_SECTION + +START_SECTION((static std::vector getMarkerIonsMassSet(const PrecursorsToMS2Adducts& pc2adducts))) +{ + // First create some test data + StringList fragment_adducts; + fragment_adducts.push_back("U:H-2O-1;U-H2O"); + NuXLParameterParsing::NucleotideToFragmentAdductMap nuc_to_frag = + NuXLParameterParsing::getTargetNucleotideToFragmentAdducts(fragment_adducts); + + set can_xl = {'U'}; + + MS2AdductsOfSinglePrecursorAdduct ms2_adducts = + NuXLParameterParsing::getFeasibleFragmentAdducts( + "U-H2O", + "C9H11N2O7P", + nuc_to_frag, + can_xl, + true, + true); + + NuXLParameterParsing::PrecursorsToMS2Adducts pc2adducts; + pc2adducts["U-H2O"] = ms2_adducts; + + vector result = + NuXLParameterParsing::getMarkerIonsMassSet(pc2adducts); + + TEST_NOT_EQUAL(result.size(), 0) // Should have marker ions + + // Test empty input + NuXLParameterParsing::PrecursorsToMS2Adducts empty_pc2adducts; + vector empty_result = + NuXLParameterParsing::getMarkerIonsMassSet(empty_pc2adducts); + + TEST_EQUAL(empty_result.empty(), true) +} +END_SECTION +*/ +START_SECTION((static PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts(const NuXLModificationMassesResult& precursor_adducts, const NucleotideToFragmentAdductMap& nucleotide_to_fragment_adducts, const std::set& can_xl, const bool always_add_default_marker_ions, const bool default_marker_ions_RNA))) +{ + // Retrieve preset for RNA-UV (U). + // This preset contains all necessary information to generate the precursor adducts and fragment adducts. + + StringList modifications; // The precursor adducts are then used to generate all feasible fragment adducts. + StringList fragment_adducts; // these are responsible for shifted fragment ions. Their fragment adducts thus determine which shifts will be observed on b-,a-,y-ions + String can_cross_link; // nucleotides that can directly cross-link + // string format: target,formula e.g. "A=C10H14N5O7P", ..., "U=C10H14N5O7P", "X=C9H13N2O8PS" where X represents tU + StringList target_nucleotides; + // string format: source->target e.g. "A->A", ..., "U->U", "U->X" + StringList mappings; + + NuXLPresets::getPresets("RNA-UV (U)", target_nucleotides, mappings, modifications, fragment_adducts, can_cross_link); + + // test preset strings + TEST_EQUAL(target_nucleotides.size(), 4) + StringList expected_target_nucleotides = { + "A=C10H14N5O7P", + "C=C9H14N3O8P", + "G=C10H14N5O8P", + "U=C9H13N2O9P" + }; + TEST_TRUE(target_nucleotides == expected_target_nucleotides); + if (target_nucleotides != expected_target_nucleotides) + { + for (const auto& t : target_nucleotides) { std::cerr << t << endl; } + } + + // list all precursor adducts (including nucleotides that can't cross-link) + StringList expected_modifications = { + "U:", + "U:-H2O", + "C:", + "C:-H2O", + "C:-NH3", + "G:", + "G:-H2O", + "G:-NH3", + "A:", + "A:-NH3" + }; + TEST_TRUE(modifications == expected_modifications); + if (modifications != expected_modifications) + { + for (const auto& m : modifications) { std::cerr << m << endl; } + } + + StringList expected_fragment_adducts = { + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + }; + + TEST_TRUE(fragment_adducts == expected_fragment_adducts); + + TEST_EQUAL(can_cross_link, "U") + + TEST_EQUAL(mappings.size(), 4) + StringList expected_mapping = { + "A->A", + "C->C", + "G->G", + "U->U" + }; + TEST_EQUAL(mappings.size(), 4) + TEST_TRUE(mappings == expected_mapping); + if (mappings != expected_mapping) + { + for (const auto& m : mappings) { std::cerr << m << endl; } + } + + // convert string to set + set can_xl; + for (const auto& c : can_cross_link) { can_xl.insert(c); } // sort and make unique + + NuXLModificationMassesResult mm = NuXLModificationsGenerator::initModificationMassesNA( + target_nucleotides, + StringList(), + can_xl, + mappings, + modifications, + "", + false, + 2); + + mm.formula2mass[""] = 0; // insert "null" modification otherwise peptides without NA will not be searched + mm.mod_combinations[""].insert("none"); + + // check content of formula2mass and ensure order is correct + StringList formula = { + "", + "C18H22N4O16P2", + "C18H23N5O15P2", + "C18H24N4O17P2", + "C18H25N5O16P2", + "C19H22N6O15P2", + "C19H22N6O16P2", + "C19H23N7O14P2", + "C19H23N7O15P2", + "C19H25N7O15P2", + "C19H25N7O16P2", + "C9H11N2O8P1", + "C9H13N2O9P1" + }; + + DoubleList mass = { + 0, + 612.051, + 611.067, + 630.061, + 629.077, + 636.062, + 652.057, + 635.078, + 651.073, + 653.088, + 669.083, + 306.025, + 324.036 + }; + + // compare using approximate double comparison due to floating point precision + for (Size i = 0; i != formula.size(); ++i) + { + TEST_REAL_SIMILAR(mm.formula2mass[formula[i]], mass[i]) + } + + std::vector expected_precursor_formula = { + "", + "C18H22N4O16P2", + "C18H23N5O15P2", + "C18H24N4O17P2", + "C18H25N5O16P2", + "C19H22N6O15P2", + "C19H22N6O16P2", + "C19H23N7O14P2", + "C19H23N7O15P2", + "C19H25N7O15P2", + "C19H25N7O16P2", + "C9H11N2O8P1", + "C9H13N2O9P1" + }; + + std::vector> expected_precursors = { + {"none"}, + {"UC-H3N1", "UU-H2O1"}, + {"CU-H2O1"}, + {"UU"}, + {"CU"}, + {"UA-H3N1"}, + {"UG-H3N1"}, + {"AU-H2O1"}, + {"GU-H2O1"}, + {"AU"}, + {"GU"}, + {"U-H2O1"}, + {"U"} + }; + + // check content of mod_combinations (order matters) + for (Size i = 0; i != expected_precursor_formula.size(); ++i) + { + TEST_EQUAL(mm.mod_combinations[expected_precursor_formula[i]].size(), expected_precursors[i].size()) + for (Size j = 0; j != expected_precursors[i].size(); ++j) + { + auto it = mm.mod_combinations[expected_precursor_formula[i]].begin(); + std::advance(it, j); + TEST_EQUAL(*it, expected_precursors[i][j]) + } + } + + // first, we determine which fragments adducts can be generated from a single nucleotide (that has no losses) + NuXLParameterParsing::NucleotideToFragmentAdductMap nucleotide_to_fragment_adducts = NuXLParameterParsing::getTargetNucleotideToFragmentAdducts(fragment_adducts); + + // check if all nucleotides are covered by the map (required to generate fragment adducts) + + std::vector>> expected_nucleotides_to_fragments = { + {'A', { + "A'-NH3", + "A'", + "A-NH3-H3PO4", + "A-H3PO4", + "A-NH3-HPO3", + "A-HPO3", + "A-NH3-H2O", + "A-H2O", + "A-NH3", + "A" + }}, + {'C', { + "C'-H2O", + "C'-NH3", + "C'", + "C-NH3-H3PO4", + "C-H3PO4", + "C-NH3-HPO3", + "C-HPO3", + "C-NH3-H2O", + "C-H2O", + "C-NH3", + "C" + }}, + {'G', { + "G'-H2O", + "G'-NH3", + "G'", + "G-NH3-H3PO4", + "G-H3PO4", + "G-NH3-HPO3", + "G-HPO3", + "G-NH3-H2O", + "G-H2O", + "G-NH3", + "G" + }}, + {'U', { + "C3O", + "U'-H2O", + "U'", + "U-H3PO4", + "U-HPO3", + "U-H2O", + "U" + }} + }; + + TEST_EQUAL(nucleotide_to_fragment_adducts.size(), expected_nucleotides_to_fragments.size()) + + for (size_t nt = 0; nt != expected_nucleotides_to_fragments.size(); ++nt) + { + // test target nucleotide formula + auto it = nucleotide_to_fragment_adducts.begin(); + std::advance(it, nt); + TEST_EQUAL(expected_nucleotides_to_fragments[nt].first, it->first); // order should match the expected target nucleotides + TEST_EQUAL(expected_nucleotides_to_fragments[nt].second.size(), it->second.size()) + if (expected_nucleotides_to_fragments[nt].second.size() != it->second.size()) + { + for (const auto& f : it->second) { std::cerr << f.name << endl; } + } + for (size_t f = 0; f != expected_nucleotides_to_fragments[nt].second.size(); ++f) + { + auto fit = it->second.begin(); + std::advance(fit, f); + // order should match exactly the expected fragments + TEST_TRUE(expected_nucleotides_to_fragments[nt].second[f] == fit->name) + } + } + + + // calculate all feasible fragment adducts from all possible precursor adducts + NuXLParameterParsing::PrecursorsToMS2Adducts all_feasible_fragment_adducts = NuXLParameterParsing::getAllFeasibleFragmentAdducts(mm, nucleotide_to_fragment_adducts, can_xl, true, true); + + // print all chemically feasible fragment adducts + std::vector>>> expected_pc2nuc2fragment_adducts = { + {"AU", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"AU-H2O1", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"CU", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"CU-H2O1", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"GU", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"GU-H2O1", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"U", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"U-H2O1", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-H2O"}}}, + {"UA-H3N1", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"UC-H3N1", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"UG-H3N1", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"UU", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"UU-H2O1", {'U', {"C3O", "U'-H2O", "U'", "U-H3PO4", "U-HPO3", "U-H2O", "U"}}}, + {"none", {'U', {}}} + }; + + TEST_EQUAL(all_feasible_fragment_adducts.size(), expected_pc2nuc2fragment_adducts.size()) + + // Compare each precursor and its associated fragments in order + auto it_expected = expected_pc2nuc2fragment_adducts.begin(); + auto it_actual = all_feasible_fragment_adducts.begin(); + + while (it_expected != expected_pc2nuc2fragment_adducts.end() && it_actual != all_feasible_fragment_adducts.end()) + { + const String& expected_precursor = it_expected->first; + const String& actual_precursor = it_actual->first; + + // Ensure the order of precursors is preserved + TEST_EQUAL(expected_precursor, actual_precursor) + + const auto& expected_adducts = it_expected->second; + const MS2AdductsOfSinglePrecursorAdduct& ms2adducts = it_actual->second; + const std::vector& nt2feasible = ms2adducts.feasible_adducts; + + if (!nt2feasible.empty()) + { + const auto& n2fsa = nt2feasible[0]; + + // Check nucleotide + TEST_EQUAL(n2fsa.first, expected_adducts.first) + + // Check fragment adducts + TEST_EQUAL(n2fsa.second.size(), expected_adducts.second.size()) + for (Size i = 0; i < expected_adducts.second.size(); ++i) + { + if (i < n2fsa.second.size()) + { + TEST_EQUAL(n2fsa.second[i].name, expected_adducts.second[i]) + } + } + } + + ++it_expected; + ++it_actual; + } +} +END_SECTION + +///////////////////////////////////////////////////////////// +///////////////////////////////////////////////////////////// +END_TEST \ No newline at end of file diff --git a/src/topp/OpenNuXL.cpp b/src/topp/OpenNuXL.cpp index e1bfa7688fa..50fd2862b9a 100644 --- a/src/topp/OpenNuXL.cpp +++ b/src/topp/OpenNuXL.cpp @@ -5096,6 +5096,7 @@ static void scoreXLIons_( isRNA = false; } } + // convert string to set for (const auto& c : can_cross_link) { can_xl_.insert(c); } // sort and make unique String sequence_restriction = getStringOption_("NuXL:sequence"); From 0d4586f99da4f9d9de5fa98f2f340b73c86c9a5f Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Tue, 25 Feb 2025 18:34:47 +0100 Subject: [PATCH 330/471] Add support for custom RNA/DNA presets in json file (#7856) * add json * minor error check * move file to share * attempt to move all presets to json * remove built in presets * remove debug output * add advanced option to OpenNuXL to specify custom presets file * Update README.md with preset usage instructions --- share/OpenMS/NUXL/README.md | 17 + share/OpenMS/NUXL/nuxl_presets.json | 1739 +++++++++++++++++ .../OpenMS/ANALYSIS/NUXL/NuXLPresets.h | 1538 +-------------- .../source/ANALYSIS/NUXL/NuXLPresets.cpp | 196 ++ src/openms/source/ANALYSIS/NUXL/sources.cmake | 1 + src/topp/OpenNuXL.cpp | 23 +- 6 files changed, 2004 insertions(+), 1510 deletions(-) create mode 100644 share/OpenMS/NUXL/README.md create mode 100644 share/OpenMS/NUXL/nuxl_presets.json create mode 100644 src/openms/source/ANALYSIS/NUXL/NuXLPresets.cpp diff --git a/share/OpenMS/NUXL/README.md b/share/OpenMS/NUXL/README.md new file mode 100644 index 00000000000..bedad098fb5 --- /dev/null +++ b/share/OpenMS/NUXL/README.md @@ -0,0 +1,17 @@ +# NuXL Custom Presets + +This directory contains custom presets for the OpenNuXL tool. These presets define the nucleotide configurations and fragment adducts used in the cross-linking analysis. + +## JSON Format + +The JSON file should contain a dictionary where each key is a preset name and each value is a dictionary with the following keys: + +- `target_nucleotides`: List of nucleotides and their empirical formulas (e.g., `"U=C9H13N2O9P"`) +- `mapping`: List of nucleotide mappings (e.g., `"U->U"`) +- `can_cross_link`: String of nucleotides that can form cross-links (e.g., `"U"` for RNA or `"T"` for DNA) +- `modifications`: List of modifications that can be applied to nucleotides (e.g., `"U:"`, `"U:-H2O"`) +- `fragment_adducts`: List of fragment adducts that can be generated from nucleotides (e.g., `"U:C9H10N2O5;U-H3PO4"`) + +## Example + +See the default `nuxl_presets.json` in the share folder for all presets for RNA and DNA. \ No newline at end of file diff --git a/share/OpenMS/NUXL/nuxl_presets.json b/share/OpenMS/NUXL/nuxl_presets.json new file mode 100644 index 00000000000..704f272193a --- /dev/null +++ b/share/OpenMS/NUXL/nuxl_presets.json @@ -0,0 +1,1739 @@ +{ + "RNA-UV (U)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "U", + "modifications": [ + "U:", + "U:-H2O", + "C:", + "C:-H2O", + "C:-NH3", + "G:", + "G:-H2O", + "G:-NH3", + "A:", + "A:-NH3" + ], + "fragment_adducts": [ + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + ] + }, + "RNA-UV (UCGA)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "UCGA", + "modifications": [ + "U:", + "U:-H2O", + "C:", + "C:-H2O", + "C:-NH3", + "G:", + "G:-H2O", + "G:-NH3", + "A:", + "A:-NH3" + ], + "fragment_adducts": [ + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + ] + }, + "RNA-UV Extended (U)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "U", + "modifications": [ + "U:", + "U:-H2O", + "U:-HPO3", + "U:-H3PO4", + "U:-HPO3-C2H3NO", + "C:", + "C:-NH3", + "C:-H2O", + "C:-HPO3", + "C:-H3PO4", + "C:-NH3-H2O", + "C:-NH3-HPO3", + "C:-NH3-H3PO4", + "G:", + "G:-H2O", + "G:-NH3", + "G:-HPO3", + "G:-H3PO4", + "G:-NH3-H2O", + "G:-NH3-HPO3", + "G:-NH3-H3PO4", + "A:", + "A:-H2O", + "A:-HPO3", + "A:-H3PO4", + "A:-NH3", + "A:-NH3-H2O", + "A:-NH3-HPO3", + "A:-NH3-H3PO4" + ], + "fragment_adducts": [ + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + ] + }, + "RNA-UV Extended (UCGA)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "UCGA", + "modifications": [ + "U:", + "U:-H2O", + "U:-HPO3", + "U:-H3PO4", + "U:-HPO3-C2H3NO", + "C:", + "C:-NH3", + "C:-H2O", + "C:-HPO3", + "C:-H3PO4", + "C:-NH3-H2O", + "C:-NH3-HPO3", + "C:-NH3-H3PO4", + "G:", + "G:-H2O", + "G:-NH3", + "G:-HPO3", + "G:-H3PO4", + "G:-NH3-H2O", + "G:-NH3-HPO3", + "G:-NH3-H3PO4", + "A:", + "A:-H2O", + "A:-HPO3", + "A:-H3PO4", + "A:-NH3", + "A:-NH3-H2O", + "A:-NH3-HPO3", + "A:-NH3-H3PO4" + ], + "fragment_adducts": [ + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + ] + }, + "RNA-UV (4SU)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P", "S=C9H13N2O8PS"], + "mapping": ["A->A", "C->C", "G->G", "U->U", "S->S"], + "can_cross_link": "S", + "modifications": [ + "S:", + "S:-H2O", + "S:-H2S", + "S:-C5H8O4", + "S:-C5H8O4-H2O", + "S:-C5H8O4-H2S" + ], + "fragment_adducts": [ + "S:C9H10N2O5;tU-H2S", + "S:C4H2N2O1;tU'-H2S", + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + ] + }, + "RNA-UV Extended (4SU)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P", "S=C9H13N2O8PS"], + "mapping": ["A->A", "C->C", "G->G", "U->U", "S->S"], + "can_cross_link": "S", + "modifications": [ + "S:", + "S:-H2O", + "S:-H3PO4", + "S:-HPO3", + "S:-H2S", + "S:+HPO3-H2S", + "S:-HPO3-H2S", + "S:+HPO3", + "S:-C5H8O4", + "S:-C5H8O4-H2O", + "S:-C5H8O4-H3PO4", + "S:-C5H8O4-HPO3", + "S:-C5H8O4-HPO3-H2S", + "S:-C5H8O4-H2S" + ], + "fragment_adducts": [ + "S:C9H10N2O5;tU-H2S", + "S:C4H2N2O1;tU'-H2S", + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + ] + }, + "RNA-UV (6SG)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P", "X=C10H14N5O7PS"], + "mapping": ["A->A", "C->C", "G->G", "U->U", "X->X"], + "can_cross_link": "X", + "modifications": [ + "X:", + "X:-H2O", + "X:-H2S", + "X:-C5H8O4", + "X:-C5H8O4-H2O", + "X:-C5H8O4-H2S" + ], + "fragment_adducts": [ + "X:C10H11N5O4;tG-H2S", + "X:C5H3N5;tG'-H2S", + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + ] + }, + "RNA-UV Extended (6SG)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P", "X=C10H14N5O7PS"], + "mapping": ["A->A", "C->C", "G->G", "U->U", "X->X"], + "can_cross_link": "X", + "modifications": [ + "X:", + "X:-H2O", + "X:-H3PO4", + "X:-HPO3", + "X:-H2S", + "X:-HPO3-H2S", + "X:-C5H8O4", + "X:-C5H8O4-H2O", + "X:-C5H8O4-HPO3", + "X:-C5H8O4-HPO3-H2S", + "X:-C5H8O4-H2S" + ], + "fragment_adducts": [ + "X:C10H11N5O4;tG-H2S", + "X:C5H3N5;tG'-H2S", + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "C:C9H14N3O8P;C", + "C:C9H11N2O8P;C-NH3", + "C:C9H12N3O7P;C-H2O", + "C:C9H9N2O7P;C-NH3-H2O", + "C:C9H13N3O5;C-HPO3", + "C:C9H11N3O4;C-H3PO4", + "C:C9H10N2O5;C-NH3-HPO3", + "C:C9H8N2O4;C-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "G:C10H14N5O8P;G", + "G:C10H12N5O7P;G-H2O", + "G:C10H11N4O8P;G-NH3", + "G:C10H9N4O7P;G-NH3-H2O", + "G:C10H13N5O5;G-HPO3", + "G:C10H11N5O4;G-H3PO4", + "G:C10H10N4O5;G-NH3-HPO3", + "G:C10H8N4O4;G-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "A:C10H14N5O7P;A", + "A:C10H12N5O6P;A-H2O", + "A:C10H11N4O7P;A-NH3", + "A:C10H9N4O6P;A-NH3-H2O", + "A:C10H13N5O4;A-HPO3", + "A:C10H11N5O3;A-H3PO4", + "A:C10H10N5O4;A-NH3-HPO3", + "A:C10H8N5O3;A-NH3-H3PO4" + ] + }, + "DNA-UV": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "d->d"], + "can_cross_link": "TCGAd", + "modifications": [ + "T:", + "T:-H2O", + "G:", + "G:-H2O", + "G:-NH3", + "A:", + "A:-NH3", + "C:", + "C:-H2O", + "C:-NH3", + "d:", + "d:-H2O" + ], + "fragment_adducts": [ + "T:C5H6N2O2;T'", + "T:C5H4N2O;T'-H2O", + "T:C10H15N2O8P;T", + "T:C10H13N2O7P;T-H2O", + "T:C10H14N2O5;T-HPO3", + "T:C10H12N2O4;T-H3PO4", + "C:C9H14N3O7P;C", + "C:C9H11N2O7P;C-NH3", + "C:C9H12N3O6P;C-H2O", + "C:C9H9N2O6P;C-NH3-H2O", + "C:C9H13N3O4;C-HPO3", + "C:C9H11N3O3;C-H3PO4", + "C:C9H10N2O4;C-NH3-HPO3", + "C:C9H8N2O3;C-NH3-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "G:C10H14N5O7P;G", + "G:C10H12N5O6P;G-H2O", + "G:C10H11N4O7P;G-NH3", + "G:C10H9N4O6P;G-NH3-H2O", + "G:C10H13N5O4;G-HPO3", + "G:C10H10N4O4;G-NH3-HPO3", + "G:C10H11N5O3;G-H3PO4", + "G:C10H8N4O3;G-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "A:C10H14N5O6P;A", + "A:C10H12N5O5P;A-H2O", + "A:C10H11N4O6P;A-NH3", + "A:C10H9N4O5P;A-NH3-H2O", + "A:C10H13N5O3;A-HPO3", + "A:C10H11N5O2;A-H3PO4", + "A:C10H10N5O3;A-NH3-HPO3", + "A:C10H8N5O2;A-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "DNA-UV Extended": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "d->d"], + "can_cross_link": "TCGAd", + "modifications": [ + "T:", + "T:-H2O", + "T:-H3PO4", + "T:-HPO3", + "C:", + "C:-H2O", + "C:-H3PO4", + "C:-HPO3", + "C:-NH3", + "C:-NH3-H2O", + "C:-NH3-HPO3", + "C:-NH3-H3PO4", + "G:", + "G:-H2O", + "G:-H3PO4", + "G:-HPO3", + "G:-NH3", + "G:-NH3-H2O", + "G:-NH3-HPO3", + "G:-NH3-H3PO4", + "A:", + "A:-NH3", + "A:-H2O", + "A:-H3PO4", + "A:-HPO3", + "A:-NH3-H2O", + "A:-NH3-HPO3", + "A:-NH3-H3PO4", + "d:", + "d:-H2O", + "d:-H3PO4", + "d:-HPO3" + ], + "fragment_adducts": [ + "T:C5H6N2O2;T'", + "T:C5H4N2O;T'-H2O", + "T:C10H15N2O8P;T", + "T:C10H13N2O7P;T-H2O", + "T:C10H14N2O5;T-HPO3", + "T:C10H12N2O4;T-H3PO4", + "C:C9H14N3O7P;C", + "C:C9H11N2O7P;C-NH3", + "C:C9H12N3O6P;C-H2O", + "C:C9H9N2O6P;C-NH3-H2O", + "C:C9H13N3O4;C-HPO3", + "C:C9H11N3O3;C-H3PO4", + "C:C9H10N2O4;C-NH3-HPO3", + "C:C9H8N2O3;C-NH3-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "G:C10H14N5O7P;G", + "G:C10H12N5O6P;G-H2O", + "G:C10H11N4O7P;G-NH3", + "G:C10H9N4O6P;G-NH3-H2O", + "G:C10H13N5O4;G-HPO3", + "G:C10H10N4O4;G-NH3-HPO3", + "G:C10H11N5O3;G-H3PO4", + "G:C10H8N4O3;G-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "A:C10H14N5O6P;A", + "A:C10H12N5O5P;A-H2O", + "A:C10H11N4O6P;A-NH3", + "A:C10H9N4O5P;A-NH3-H2O", + "A:C10H13N5O3;A-HPO3", + "A:C10H11N5O2;A-H3PO4", + "A:C10H10N5O3;A-NH3-HPO3", + "A:C10H8N5O2;A-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "DNA-UV (BrU)": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "B=C9H11N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "B->B", "d->d"], + "can_cross_link": "B", + "modifications": [ + "T:", + "T:-H2O", + "B:", + "B:-H2O", + "G:", + "G:-H2O", + "G:-NH3", + "A:", + "A:-NH3", + "C:", + "C:-H2O", + "C:-NH3", + "d:", + "d:-H2O" + ], + "fragment_adducts": [ + "T:C5H6N2O2;T'", + "T:C5H4N2O;T'-H2O", + "T:C10H15N2O8P;T", + "T:C10H13N2O7P;T-H2O", + "T:C10H14N2O5;T-HPO3", + "T:C10H12N2O4;T-H3PO4", + "B:C4H2N2O2;B'", + "B:C4N2O;B'-H2O", + "B:C9H11N2O8P;B", + "B:C9H9N2O7P;B-H2O", + "B:C9H10N2O5;B-HPO3", + "B:C9H8N2O4;B-H3PO4", + "C:C9H14N3O7P;C", + "C:C9H11N2O7P;C-NH3", + "C:C9H12N3O6P;C-H2O", + "C:C9H9N2O6P;C-NH3-H2O", + "C:C9H13N3O4;C-HPO3", + "C:C9H11N3O3;C-H3PO4", + "C:C9H10N2O4;C-NH3-HPO3", + "C:C9H8N2O3;C-NH3-H3PO4", + "C:C4H5N3O;C'", + "C:C4H3N3;C'-H2O", + "C:C4H2N2O;C'-NH3", + "G:C10H14N5O7P;G", + "G:C10H12N5O6P;G-H2O", + "G:C10H11N4O7P;G-NH3", + "G:C10H9N4O6P;G-NH3-H2O", + "G:C10H13N5O4;G-HPO3", + "G:C10H10N4O4;G-NH3-HPO3", + "G:C10H11N5O3;G-H3PO4", + "G:C10H8N4O3;G-NH3-H3PO4", + "G:C5H5N5O;G'", + "G:C5H3N5;G'-H2O", + "G:C5H2N4O;G'-NH3", + "A:C10H14N5O6P;A", + "A:C10H12N5O5P;A-H2O", + "A:C10H11N4O6P;A-NH3", + "A:C10H9N4O5P;A-NH3-H2O", + "A:C10H13N5O3;A-HPO3", + "A:C10H11N5O2;A-H3PO4", + "A:C10H10N5O3;A-NH3-HPO3", + "A:C10H8N5O2;A-NH3-H3PO4", + "A:C5H5N5;A'", + "A:C5H2N4;A'-NH3", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "RNA-DEB": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "UCGA", + "modifications": [ + "U:+C4H6O2", + "G:+C4H6O2", + "C:+C4H6O2", + "A:+C4H6O2" + ], + "fragment_adducts": [ + "U:C4H6O2;DEB", + "U:C4H4O;DEB-H2O", + "U:C7H6O3;DEB+C3O", + "U:C8H10N2O4;DEB+U'", + "U:C8H8N2O3;DEB+U'-H2O", + "U:C13H19N2O11P1;DEB+U", + "U:C13H17N2O10P1;DEB+U-H2O", + "U:C13H18N2O8;DEB+U-HPO3", + "U:C13H16N2O7;DEB+U-H3PO4", + "G:C4H6O2;DEB", + "G:C4H4O;DEB-H2O", + "G:C9H11N5O3;DEB+G'", + "G:C8H9N5O3;DEB+G'-H2O", + "G:C9H8N4O3;DEB+G'-NH3", + "G:C14H20N5O10P1;DEB+G", + "G:C14H18N5O9P1;DEB+G-H2O", + "G:C14H17N4O10P1;DEB+G-NH3", + "G:C14H19N5O7;DEB+G-HPO3", + "G:C14H17N5O6;DEB+G-H3PO4", + "G:C14H16N4O7;DEB+G-NH3-HPO3", + "G:C14H14N4O6;DEB+G-NH3-H3PO4", + "G:C14H15N4O9P1;DEB+G-NH3-H2O", + "C:C4H6O2;DEB", + "C:C4H4O;DEB-H2O", + "C:C8H11N3O3;DEB+C'", + "C:C8H9N3O2;DEB+C'-H2O", + "C:C8H8N2O3;DEB+C'-NH3", + "C:C13H20N3O10P1;DEB+C", + "C:C13H18N3O9P1;DEB+C-H2O", + "C:C13H17N2O10P1;DEB+C-NH3", + "C:C13H19N3O7;DEB+C-HPO3", + "C:C13H17N3O6;DEB+C-H3PO4", + "C:C13H16N2O7;DEB+C-NH3-HPO3", + "C:C13H14N2O6;DEB+C-NH3-H3PO4", + "C:C13H15N2O9P1;DEB+C-NH3-H2O", + "A:C4H6O2;DEB", + "A:C4H4O;DEB-H2O", + "A:C9H11N5O2;DEB+A'", + "A:C9H17N4O;DEB+A'-NH3", + "A:C14H20N5O9P1;DEB+A", + "A:C14H18N5O8P1;DEB+A-H2O", + "A:C14H17N4O9P1;DEB+A-NH3", + "A:C14H19N5O6;DEB+A-HPO3", + "A:C14H17N5O5;DEB+A-H3PO4", + "A:C14H16N4O6;DEB+A-NH3-HPO3", + "A:C14H14N4O5;DEB+A-NH3-H3PO4", + "A:C14H15N4O8P1;DEB+A-NH3-H2O" + ] + }, + "RNA-DEB Extended": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "UCGA", + "modifications": [ + "U:+C4H6O2", + "U:+C4H6O2-H2O", + "U:+C4H6O2-HPO3", + "U:+C4H6O2-H3PO4", + "U:+C4H6O2-H2O-H2O", + "U:+C4H6O2-H3PO4-H2O", + "G:+C4H6O2", + "G:+C4H6O2-H2O", + "G:+C4H6O2-HPO3", + "G:+C4H6O2-H3PO4", + "G:+C4H6O2-H2O-H2O", + "G:+C4H6O2-H3PO4-H2O", + "G:+C4H6O2-NH3", + "G:+C4H6O2-NH3-H2O", + "G:+C4H602-NH3-HPO3", + "G:+C4H6O2-NH3-H3PO4", + "C:+C4H6O2", + "C:+C4H6O2-H2O", + "C:+C4H6O2-HPO3", + "C:+C4H6O2-H3PO4", + "C:+C4H6O2-H2O-H2O", + "C:+C4H6O2-H3PO4-H2O", + "C:+C4H6O2-NH3", + "C:+C4H6O2-NH3-H2O", + "C:+C4H602-NH3-HPO3", + "C:+C4H6O2-NH3-H3PO4", + "A:+C4H6O2", + "A:+C4H6O2-H2O", + "A:+C4H6O2-HPO3", + "A:+C4H6O2-H3PO4", + "A:+C4H6O2-NH3", + "A:+C4H6O2-NH3-H2O", + "A:+C4H6O2-NH3-HPO3", + "A:+C4H6O2-NH3-H3PO4" + ], + "fragment_adducts": [ + "U:C4H6O2;DEB", + "U:C4H4O;DEB-H2O", + "U:C7H6O3;DEB+C3O", + "U:C8H10N2O4;DEB+U'", + "U:C8H8N2O3;DEB+U'-H2O", + "U:C13H19N2O11P1;DEB+U", + "U:C13H17N2O10P1;DEB+U-H2O", + "U:C13H18N2O8;DEB+U-HPO3", + "U:C13H16N2O7;DEB+U-H3PO4", + "G:C4H6O2;DEB", + "G:C4H4O;DEB-H2O", + "G:C9H11N5O3;DEB+G'", + "G:C8H9N5O3;DEB+G'-H2O", + "G:C9H8N4O3;DEB+G'-NH3", + "G:C14H20N5O10P1;DEB+G", + "G:C14H18N5O9P1;DEB+G-H2O", + "G:C14H17N4O10P1;DEB+G-NH3", + "G:C14H19N5O7;DEB+G-HPO3", + "G:C14H17N5O6;DEB+G-H3PO4", + "G:C14H16N4O7;DEB+G-NH3-HPO3", + "G:C14H14N4O6;DEB+G-NH3-H3PO4", + "G:C14H15N4O9P1;DEB+G-NH3-H2O", + "C:C4H6O2;DEB", + "C:C4H4O;DEB-H2O", + "C:C8H11N3O3;DEB+C'", + "C:C8H9N3O2;DEB+C'-H2O", + "C:C8H8N2O3;DEB+C'-NH3", + "C:C13H20N3O10P1;DEB+C", + "C:C13H18N3O9P1;DEB+C-H2O", + "C:C13H17N2O10P1;DEB+C-NH3", + "C:C13H19N3O7;DEB+C-HPO3", + "C:C13H17N3O6;DEB+C-H3PO4", + "C:C13H16N2O7;DEB+C-NH3-HPO3", + "C:C13H14N2O6;DEB+C-NH3-H3PO4", + "C:C13H15N2O9P1;DEB+C-NH3-H2O", + "A:C4H6O2;DEB", + "A:C4H4O;DEB-H2O", + "A:C9H11N5O2;DEB+A'", + "A:C9H17N4O;DEB+A'-NH3", + "A:C14H20N5O9P1;DEB+A", + "A:C14H18N5O8P1;DEB+A-H2O", + "A:C14H17N4O9P1;DEB+A-NH3", + "A:C14H19N5O6;DEB+A-HPO3", + "A:C14H17N5O5;DEB+A-H3PO4", + "A:C14H16N4O6;DEB+A-NH3-HPO3", + "A:C14H14N4O5;DEB+A-NH3-H3PO4", + "A:C14H15N4O8P1;DEB+A-NH3-H2O" + ] + }, + "DNA-DEB": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "d->d"], + "can_cross_link": "TCGAd", + "modifications": [ + "T:+C4H6O2", + "G:+C4H6O2", + "C:+C4H6O2", + "A:+C4H6O2", + "d:", + "d:-H2O" + ], + "fragment_adducts": [ + "T:C4H6O2;DEB", + "T:C4H4O;DEB-H2O", + "T:C9H12N2O4;DEB+T'", + "T:C9H10N2O3;DEB+T'-H2O", + "T:C14H21N2O10P1;DEB+T", + "T:C14H19N2O9P1;DEB+T-H2O", + "T:C14H20N2O7;DEB+T-HPO3", + "T:C14H18N2O6;DEB+T-H3PO4", + "C:C4H6O2;DEB", + "C:C4H4O;DEB-H2O", + "C:C8H11N3O3;DEB+C'", + "C:C8H8N2O3;DEB+C'-NH3", + "C:C8H9N3O2;DEB+C'-H2O", + "C:C13H20N3O9P1;DEB+C", + "C:C13H17N2O9P1;DEB+C-NH3", + "C:C13H18N3O8P1;DEB+C-H2O", + "C:C13H19N3O6;DEB+C-HPO3", + "C:C13H17N3O5;DEB+C-H3PO4", + "C:C13H16N2O6;DEB+C-NH3-HPO3", + "C:C13H14N2O5;DEB+C-NH3-H3PO4", + "C:C13H15N2O8P1;DEB+C-NH3-H2O", + "G:C4H6O2;DEB", + "G:C4H4O;DEB-H2O", + "G:C9H11N5O3;DEB+G'", + "G:C9H8N4O3;DEB+G'-NH3", + "G:C9H9N5O2;DEB+G'-H2O", + "G:C14H20N5O9P1;DEB+G", + "G:C14H17N4O9P1;DEB+G-NH3", + "G:C14H18N5O8P1;DEB+G-H2O", + "G:C14H19N5O6;DEB+G-HPO3", + "G:C14H17N5O5;DEB+G-H3PO4", + "G:C14H16N4O6;DEB+G-NH3-HPO3", + "G:C14H14N4O5;DEB+G-NH3-H3PO4", + "G:C14H15N4O8P1;DEB+G-NH3-H2O", + "A:C4H6O2;DEB", + "A:C4H4O;DEB-H2O", + "A:C9H11N5O2;DEB+A'", + "A:C9H8N4O2;DEB+A'-NH3", + "A:C14H20N5O8P1;DEB+A", + "A:C14H17N4O8P1;DEB+A-NH3", + "A:C14H18N5O7P1;DEB+A-H2O", + "A:C14H19N5O5;DEB+A-HPO3", + "A:C14H17N5O4;DEB+A-H3PO4", + "A:C14H16N4O5;DEB+A-NH3-HPO3", + "A:C14H14N4O4;DEB+A-NH3-H3PO4", + "A:C14H15N4O7P1;DEB+A-NH3-H2O", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "DNA-DEB Extended": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "d->d"], + "can_cross_link": "TCGAd", + "modifications": [ + "T:+C4H6O2", + "T:+C4H6O2-H2O", + "T:+C4H6O2-HPO3", + "T:+C4H6O2-H3PO4", + "T:+C4H6O2-H2O-H2O", + "T:+C4H6O2-H3PO4-H2O", + "G:+C4H6O2", + "G:+C4H6O2-H2O", + "G:+C4H6O2-HPO3", + "G:+C4H6O2-H3PO4", + "G:+C4H6O2-H2O-H2O", + "G:+C4H6O2-H3PO4-H2O", + "G:+C4H6O2-NH3", + "G:+C4H6O2-NH3-H2O", + "G:+C4H6O2-NH3-HPO3", + "G:+C4H6O2-NH3-H3PO4", + "C:+C4H6O2", + "C:+C4H6O2-H2O", + "C:+C4H6O2-HPO3", + "C:+C4H6O2-H3PO4", + "C:+C4H6O2-H2O-H2O", + "C:+C4H6O2-H3PO4-H2O", + "C:+C4H6O2-NH3-H2O", + "C:+C4H6O2-NH3", + "C:+C4H6O2-NH3-HPO3", + "C:+C4H6O2-NH3-H3PO4", + "A:+C4H6O2", + "A:+C4H6O2-H2O", + "A:+C4H6O2-H3PO4", + "A:+C4H6O2-HPO3", + "A:+C4H6O2-NH3", + "A:+C4H6O2-NH3-H2O", + "A:+C4H6O2-NH3-HPO3", + "A:+C4H6O2-NH3-H3PO4", + "d:", + "d:-H2O", + "d:-H3PO4", + "d:-HPO3" + ], + "fragment_adducts": [ + "T:C4H6O2;DEB", + "T:C4H4O;DEB-H2O", + "T:C9H12N2O4;DEB+T'", + "T:C9H10N2O3;DEB+T'-H2O", + "T:C14H21N2O10P1;DEB+T", + "T:C14H19N2O9P1;DEB+T-H2O", + "T:C14H20N2O7;DEB+T-HPO3", + "T:C14H18N2O6;DEB+T-H3PO4", + "C:C4H6O2;DEB", + "C:C4H4O;DEB-H2O", + "C:C8H11N3O3;DEB+C'", + "C:C8H8N2O3;DEB+C'-NH3", + "C:C8H9N3O2;DEB+C'-H2O", + "C:C13H20N3O9P1;DEB+C", + "C:C13H17N2O9P1;DEB+C-NH3", + "C:C13H18N3O8P1;DEB+C-H2O", + "C:C13H19N3O6;DEB+C-HPO3", + "C:C13H17N3O5;DEB+C-H3PO4", + "C:C13H16N2O6;DEB+C-NH3-HPO3", + "C:C13H14N2O5;DEB+C-NH3-H3PO4", + "C:C13H15N2O8P1;DEB+C-NH3-H2O", + "G:C4H6O2;DEB", + "G:C4H4O;DEB-H2O", + "G:C9H11N5O3;DEB+G'", + "G:C9H8N4O3;DEB+G'-NH3", + "G:C9H9N5O2;DEB+G'-H2O", + "G:C14H20N5O9P1;DEB+G", + "G:C14H17N4O9P1;DEB+G-NH3", + "G:C14H18N5O8P1;DEB+G-H2O", + "G:C14H19N5O6;DEB+G-HPO3", + "G:C14H17N5O5;DEB+G-H3PO4", + "G:C14H16N4O6;DEB+G-NH3-HPO3", + "G:C14H14N4O5;DEB+G-NH3-H3PO4", + "G:C14H15N4O8P1;DEB+G-NH3-H2O", + "A:C4H6O2;DEB", + "A:C4H4O;DEB-H2O", + "A:C9H11N5O2;DEB+A'", + "A:C9H8N4O2;DEB+A'-NH3", + "A:C14H20N5O8P1;DEB+A", + "A:C14H17N4O8P1;DEB+A-NH3", + "A:C14H18N5O7P1;DEB+A-H2O", + "A:C14H19N5O5;DEB+A-HPO3", + "A:C14H17N5O4;DEB+A-H3PO4", + "A:C14H16N4O5;DEB+A-NH3-HPO3", + "A:C14H14N4O4;DEB+A-NH3-H3PO4", + "A:C14H15N4O7P1;DEB+A-NH3-H2O", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "DNA-NM": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "d->d"], + "can_cross_link": "TCGAd", + "modifications": [ + "T:+C5H9N1", + "G:+C5H9N1", + "C:+C5H9N1", + "A:+C5H9N1", + "d:", + "d:-H2O" + ], + "fragment_adducts": [ + "T:C5H9N1;NM", + "T:C15H24N3O8P1;NM+T", + "T:C15H22N3O7P1;NM+T-H2O", + "T:C15H23N3O5;NM+T-HPO3", + "T:C15H21N3O4;NM+T-H3PO4", + "T:C10H15N3O2;NM+T'", + "T:C10H13N3O1;NM+T'-H2O", + "C:C5H9N;NM", + "C:C9H14N4O1;NM+C'", + "C:C9H11N3O1;NM+C'-NH3", + "C:C9H12N4;NM+C'-H2O", + "C:C14H23N4O7P1;NM+C", + "C:C14H21N4O6P1;NM+C-H2O", + "C:C14H20N3O7P1;NM+C-NH3", + "C:C14H18N3O6P1;NM+C-NH3-H2O", + "C:C14H20N4O3;NM+C-H3PO4", + "C:C14H22N4O4;NM+C-HPO3", + "C:C14H19N3O4;NM+C-NH3-HPO3", + "C:C14H17N3O3;NM+C-NH3-H3PO4", + "G:C5H9N1;NM", + "G:C10H14N6O1;NM+G'", + "G:C10H12N6;NM+G'-H2O", + "G:C10H11N5O1;NM+G'-NH3", + "G:C15H23N6O7P1;NM+G", + "G:C15H21N6O6P1;NM+G-H2O", + "G:C15H22N6O4;NM+G-HPO3", + "G:C15H20N6O3;NM+G-H3PO4", + "G:C15H20N5O7P1;NM+G-NH3", + "G:C15H18N5O6P1;NM+G-NH3-H2O", + "G:C15H19N5O4;NM+G-NH3-HPO3", + "G:C15H17N5O3;NM+G-NH3-H3PO4", + "A:C5H9N1;NM", + "A:C10H14N6;NM+A'", + "A:C10H11N5;NM+A'-NH3", + "A:C15H23N6O6P1;NM+A", + "A:C15H20N6O2;NM+A-H3PO4", + "A:C15H21N6O5P1;NM+A-H2O", + "A:C15H22N6O3;NM+A-HPO3", + "A:C15H20N5O6P1;NM+A-NH3", + "A:C15H18N5O5P1;NM+A-NH3-H2O", + "A:C15H19N5O3;NM+A-NH3-HPO3", + "A:C15H17N5O2;NM+A-NH3-H3PO4", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "DNA-NM Extended": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "d->d"], + "can_cross_link": "TCGAd", + "modifications": [ + "T:+C5H9N1", + "T:+C5H9N1-H2O", + "T:+C5H9N1-HPO3", + "T:+C5H9N1-H3PO4", + "T:+C5H9N1-H2O-H2O", + "T:+C5H9N1-H3PO4-H2O", + "G:+C5H9N1", + "G:+C5H9N1-H2O", + "G:+C5H9N1-HPO3", + "G:+C5H9N1-H3PO4", + "G:+C5H9N1-H2O-H2O", + "G:+C5H9N1-H3PO4-H2O", + "G:+C5H9N1-NH3", + "G:+C5H9N1-NH3-H2O", + "G:+C5H9N1-NH3-HPO3", + "G:+C5H9N1-NH3-H3PO4", + "C:+C5H9N1", + "C:+C5H9N1-H2O", + "C:+C5H9N1-HPO3", + "C:+C5H9N1-H3PO4", + "C:+C5H9N1-H2O-H2O", + "C:+C5H9N1-H3PO4-H2O", + "C:+C5H9N1-NH3", + "C:+C5H9N1-NH3-HPO3", + "C:+C5H9N1-NH3-H2O", + "C:+C5H9N1-NH3-H3PO4", + "A:+C5H9N1", + "A:+C5H9N1-HPO3", + "A:+C5H9N1-H2O", + "A:+C5H9N1-H3PO4", + "A:+C5H9N1-NH3", + "A:+C5H9N1-NH3-HPO3", + "A:+C5H9N1-NH3-H2O", + "A:+C5H9N1-NH3-H3PO4", + "d:", + "d:-H2O", + "d:-H3PO4", + "d:-HPO3" + ], + "fragment_adducts": [ + "T:C5H9N1;NM", + "T:C15H24N3O8P1;NM+T", + "T:C15H22N3O7P1;NM+T-H2O", + "T:C15H23N3O5;NM+T-HPO3", + "T:C15H21N3O4;NM+T-H3PO4", + "T:C10H15N3O2;NM+T'", + "T:C10H13N3O1;NM+T'-H2O", + "C:C5H9N;NM", + "C:C9H14N4O1;NM+C'", + "C:C9H11N3O1;NM+C'-NH3", + "C:C9H12N4;NM+C'-H2O", + "C:C14H23N4O7P1;NM+C", + "C:C14H21N4O6P1;NM+C-H2O", + "C:C14H20N3O7P1;NM+C-NH3", + "C:C14H18N3O6P1;NM+C-NH3-H2O", + "C:C14H20N4O3;NM+C-H3PO4", + "C:C14H22N4O4;NM+C-HPO3", + "C:C14H19N3O4;NM+C-NH3-HPO3", + "C:C14H17N3O3;NM+C-NH3-H3PO4", + "G:C5H9N1;NM", + "G:C10H14N6O1;NM+G'", + "G:C10H12N6;NM+G'-H2O", + "G:C10H11N5O1;NM+G'-NH3", + "G:C15H23N6O7P1;NM+G", + "G:C15H21N6O6P1;NM+G-H2O", + "G:C15H22N6O4;NM+G-HPO3", + "G:C15H20N6O3;NM+G-H3PO4", + "G:C15H20N5O7P1;NM+G-NH3", + "G:C15H18N5O6P1;NM+G-NH3-H2O", + "G:C15H19N5O4;NM+G-NH3-HPO3", + "G:C15H17N5O3;NM+G-NH3-H3PO4", + "A:C5H9N1;NM", + "A:C10H14N6;NM+A'", + "A:C10H11N5;NM+A'-NH3", + "A:C15H23N6O6P1;NM+A", + "A:C15H20N6O2;NM+A-H3PO4", + "A:C15H21N6O5P1;NM+A-H2O", + "A:C15H22N6O3;NM+A-HPO3", + "A:C15H20N5O6P1;NM+A-NH3", + "A:C15H18N5O5P1;NM+A-NH3-H2O", + "A:C15H19N5O3;NM+A-NH3-HPO3", + "A:C15H17N5O2;NM+A-NH3-H3PO4", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "RNA-NM": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "UCGA", + "modifications": [ + "U:+C5H9N1", + "G:+C5H9N1", + "C:+C5H9N1", + "A:+C5H9N1" + ], + "fragment_adducts": [ + "U:C5H9N1;NM", + "U:C8H9N1O1;NM+C3O", + "U:C14H22N3O9P1;NM+U", + "U:C14H20N3O8P1;NM+U-H2O", + "U:C14H21N3O6;NM+U-HPO3", + "U:C14H19N3O5;NM+U-H3PO4", + "U:C9H13N3O2;NM+U'", + "U:C9H11N3O1;NM+U'-H2O", + "C:C5H9N1;NM", + "C:C14H23N4O8P1;NM+C", + "C:C14H21N4O7P1;NM+C-H2O", + "C:C14H20N3O8P1;NM+C-NH3", + "C:C14H22N4O5;NM+C-HPO3", + "C:C14H20N4O4;NM+C-H3PO4", + "C:C14H19N3O5;NM+C-NH3-HPO3", + "C:C14H17N3O4;NM+C-NH3-H3PO4", + "C:C9H14N4O1;NM+C'", + "C:C9H12N4;NM+C'-H2O", + "C:C9H11N3O1;NM+C'-NH3", + "C:C14H18N3O7P1;NM+C-NH3-H2O", + "G:C5H9N1;NM", + "G:C15H23N6O8P1;NM+G", + "G:C15H21N6O7P1;NM+G-H2O", + "G:C15H20N5O8P1;NM+G-NH3", + "G:C15H22N6O5;NM+G-HPO3", + "G:C15H20N6O4;NM+G-H3PO4", + "G:C15H19N5O5;NM+G-NH3-HPO3", + "G:C15H17N5O4;NM+G-NH3-H3PO4", + "G:C10H14N6O1;NM+G'", + "G:C10H12N6;NM+G'-H2O", + "G:C10H14N6O1;NM+G'-NH3", + "G:C15H18N5O7P1;NM+G-NH3-H2O", + "A:C5H9N1;NM", + "A:C15H23N6O7P1;NM+A", + "A:C15H21N6O6P1;NM+A-H2O", + "A:C15H20N5O7P1;NM+A-NH3", + "A:C15H22N6O4;NM+A-HPO3", + "A:C15H20N6O3;NM+A-H3PO4", + "A:C15H19N5O4;NM+A-NH3-HPO3", + "A:C15H17N5O3;NM+A-NH3-H3PO4", + "A:C10H14N6;NM+A'", + "A:C10H11N5;NM+A'-NH3", + "A:C15H18N5O6P1;NM+A-NH3-H2O" + ] + }, + "RNA-NM Extended": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "UCGA", + "modifications": [ + "U:+C5H9N1", + "U:+C5H9N1-HPO3", + "U:+C5H9N1-H2O", + "U:+C5H9N1-H3PO4", + "U:+C5H9N1-H2O-H2O", + "U:+C5H9N1-H3PO4-H2O", + "G:+C5H9N1", + "G:+C5H9N1-HPO3", + "G:+C5H9N1-H2O", + "G:+C5H9N1-H3PO4", + "G:+C5H9N1-H2O-H2O", + "G:+C5H9N1-H3PO4-H2O", + "G:+C5H9N1-NH3", + "G:+C5H9N1-NH3-H2O", + "G:+C5H9N1-NH3-HPO3", + "G:+C5H9N1-NH3-H3PO4", + "C:+C5H9N1", + "C:+C5H9N1-HPO3", + "C:+C5H9N1-H2O", + "C:+C5H9N1-H3PO4", + "C:+C5H9N1-H2O-H2O", + "C:+C5H9N1-H3PO4-H2O", + "C:+C5H9N1-NH3", + "C:+C5H9N1-NH3-H2O", + "C:+C5H9N1-NH3-HPO3", + "C:+C5H9N1-NH3-H3PO4", + "A:+C5H9N1", + "A:+C5H9N1-HPO3", + "A:+C5H9N1-H2O", + "A:+C5H9N1-H3PO4", + "A:+C5H9N1-NH3", + "A:+C5H9N1-NH3-H2O", + "A:+C5H9N1-NH3-HPO3", + "A:+C5H9N1-NH3-H3PO4" + ], + "fragment_adducts": [ + "U:C5H9N1;NM", + "U:C8H9N1O1;NM+C3O", + "U:C14H22N3O9P1;NM+U", + "U:C14H20N3O8P1;NM+U-H2O", + "U:C14H21N3O6;NM+U-HPO3", + "U:C14H19N3O5;NM+U-H3PO4", + "U:C9H13N3O2;NM+U'", + "U:C9H11N3O1;NM+U'-H2O", + "C:C5H9N1;NM", + "C:C14H23N4O8P1;NM+C", + "C:C14H21N4O7P1;NM+C-H2O", + "C:C14H20N3O8P1;NM+C-NH3", + "C:C14H22N4O5;NM+C-HPO3", + "C:C14H20N4O4;NM+C-H3PO4", + "C:C14H19N3O5;NM+C-NH3-HPO3", + "C:C14H17N3O4;NM+C-NH3-H3PO4", + "C:C9H14N4O1;NM+C'", + "C:C9H12N4;NM+C'-H2O", + "C:C9H11N3O1;NM+C'-NH3", + "C:C14H18N3O7P1;NM+C-NH3-H2O", + "G:C5H9N1;NM", + "G:C15H23N6O8P1;NM+G", + "G:C15H21N6O7P1;NM+G-H2O", + "G:C15H20N5O8P1;NM+G-NH3", + "G:C15H22N6O5;NM+G-HPO3", + "G:C15H20N6O4;NM+G-H3PO4", + "G:C15H19N5O5;NM+G-NH3-HPO3", + "G:C15H17N5O4;NM+G-NH3-H3PO4", + "G:C10H14N6O1;NM+G'", + "G:C10H12N6;NM+G'-H2O", + "G:C10H14N6O1;NM+G'-NH3", + "G:C15H18N5O7P1;NM+G-NH3-H2O", + "A:C5H9N1;NM", + "A:C15H23N6O7P1;NM+A", + "A:C15H21N6O6P1;NM+A-H2O", + "A:C15H20N5O7P1;NM+A-NH3", + "A:C15H22N6O4;NM+A-HPO3", + "A:C15H20N6O3;NM+A-H3PO4", + "A:C15H19N5O4;NM+A-NH3-HPO3", + "A:C15H17N5O3;NM+A-NH3-H3PO4", + "A:C10H14N6;NM+A'", + "A:C10H11N5;NM+A'-NH3", + "A:C15H18N5O6P1;NM+A-NH3-H2O" + ] + }, + "RNA-NM Extended (+H2O)": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "UCGA", + "modifications": [ + "U:+C5H9N1", + "U:+C5H9N1-HPO3", + "U:+C5H9N1-H2O", + "U:+C5H9N1-H3PO4", + "U:+C5H9N1-H2O-H2O", + "U:+C5H9N1-H3PO4-H2O", + "G:+C5H9N1", + "G:+C5H9N1-HPO3", + "G:+C5H9N1-H2O", + "G:+C5H9N1-H3PO4", + "G:+C5H9N1-H2O-H2O", + "G:+C5H9N1-H3PO4-H2O", + "G:+C5H9N1-NH3", + "G:+C5H9N1-NH3-H2O", + "G:+C5H9N1-NH3-HPO3", + "G:+C5H9N1-NH3-H3PO4", + "G:+C5H9N1+H2O", + "C:+C5H9N1", + "C:+C5H9N1-HPO3", + "C:+C5H9N1-H2O", + "C:+C5H9N1-H3PO4", + "C:+C5H9N1-H2O-H2O", + "C:+C5H9N1-H3PO4-H2O", + "C:+C5H9N1-NH3", + "C:+C5H9N1-NH3-H2O", + "C:+C5H9N1-NH3-HPO3", + "C:+C5H9N1-NH3-H3PO4", + "A:+C5H9N1", + "A:+C5H9N1-HPO3", + "A:+C5H9N1-H2O", + "A:+C5H9N1-H3PO4", + "A:+C5H9N1-NH3", + "A:+C5H9N1-NH3-H2O", + "A:+C5H9N1-NH3-HPO3", + "A:+C5H9N1-NH3-H3PO4", + "A:+C5H9N1+H2O" + ], + "fragment_adducts": [ + "U:C5H9N1;NM", + "U:C8H9N1O1;NM+C3O", + "U:C14H22N3O9P1;NM+U", + "U:C14H20N3O8P1;NM+U-H2O", + "U:C14H21N3O6;NM+U-HPO3", + "U:C14H19N3O5;NM+U-H3PO4", + "U:C9H13N3O2;NM+U'", + "U:C9H11N3O1;NM+U'-H2O", + "C:C5H9N1;NM", + "C:C14H23N4O8P1;NM+C", + "C:C14H21N4O7P1;NM+C-H2O", + "C:C14H20N3O8P1;NM+C-NH3", + "C:C14H22N4O5;NM+C-HPO3", + "C:C14H20N4O4;NM+C-H3PO4", + "C:C14H19N3O5;NM+C-NH3-HPO3", + "C:C14H17N3O4;NM+C-NH3-H3PO4", + "C:C9H14N4O1;NM+C'", + "C:C9H12N4;NM+C'-H2O", + "C:C9H11N3O1;NM+C'-NH3", + "C:C14H18N3O7P1;NM+C-NH3-H2O", + "G:C5H9N1;NM", + "G:C15H23N6O8P1;NM+G", + "G:C15H21N6O7P1;NM+G-H2O", + "G:C15H25N6O9P1;NM+G+H2O", + "G:C15H20N5O8P1;NM+G-NH3", + "G:C15H22N6O5;NM+G-HPO3", + "G:C15H20N6O4;NM+G-H3PO4", + "G:C15H19N5O5;NM+G-NH3-HPO3", + "G:C15H17N5O4;NM+G-NH3-H3PO4", + "G:C10H14N6O1;NM+G'", + "G:C10H12N6;NM+G'-H2O", + "G:C10H16N6O2;NM+G'+H2O", + "G:C10H14N6O1;NM+G'-NH3", + "G:C15H18N5O7P1;NM+G-NH3-H2O", + "A:C5H9N1;NM", + "A:C15H23N6O7P1;NM+A", + "A:C15H21N6O6P1;NM+A-H2O", + "A:C15H25N6O8P1;NM+A+H2O", + "A:C15H20N5O7P1;NM+A-NH3", + "A:C15H22N6O4;NM+A-HPO3", + "A:C15H20N6O3;NM+A-H3PO4", + "A:C15H19N5O4;NM+A-NH3-HPO3", + "A:C15H17N5O3;NM+A-NH3-H3PO4", + "A:C10H14N6;NM+A'", + "A:C10H11N5;NM+A'-NH3", + "A:C10H16N6O;NM+A'+H2O", + "A:C15H18N5O6P1;NM+A-NH3-H2O" + ] + }, + "RNA-FA": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "CGA", + "modifications": [ + "G:+C", + "G:+C-HPO3", + "G:+C-H3PO4", + "G:+C-H2O", + "C:+C", + "C:+C-H2O", + "C:+C-HPO3", + "C:+C-H3PO4", + "A:+C", + "A:+C-HPO3", + "A:+C-H3PO4", + "A:+C-H2O" + ], + "fragment_adducts": [ + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "G:C;FA", + "G:C5H5N5O;G'", + "G:C10H14N5O8P;G", + "G:C6H5N5O;G'+FA", + "G:C11H14N5O8P;G+FA", + "G:C11H12N5O7P;G+FA-H2O", + "G:C11H11N5O4;G+FA-H3PO4", + "G:C11H13N5O5;G+FA-HPO3", + "G:C7H5N5O;G'+2FA", + "G:C12H14N5O8P;G+2FA", + "G:C12H12N5O7P;G+2FA-H2O", + "G:C12H11N5O4;G+2FA-H3PO4", + "G:C12H13N5O5;G+2FA-HPO3", + "C:C;FA", + "C:C4H5N3O;C'", + "C:C9H14N3O8P;C", + "C:C5H5N3O;C'+FA", + "C:C10H14N3O8P;C+FA", + "C:C10H13N3O5;C+FA-HPO3", + "C:C10H12N3O7P;C+FA-H2O", + "C:C10H11N3O4;C+FA-H3PO4", + "C:C6H5N3O;C'+2FA", + "C:C11H14N3O8P;C+2FA", + "C:C11H13N3O5;C+2FA-HPO3", + "C:C11H12N3O7P;C+2FA-H2O", + "C:C11H11N3O4;C+2FA-H3PO4", + "A:C;FA", + "A:C5H5N5;A'", + "A:C10H14N5O7P;A", + "A:C6H5N5;A'+FA", + "A:C11H14N5O7P;A+FA", + "A:C11H13N5O4;A+FA-HPO3", + "A:C11H12N5O6P;A+FA-H2O", + "A:C11H11N5O3;A+FA-H3PO4", + "A:C7H5N5;A'+2FA", + "A:C12H14N5O7P;A+2FA", + "A:C12H13N5O4;A+2FA-HPO3", + "A:C12H12N5O6P;A+2FA-H2O", + "A:C12H11N5O3;A+2FA-H3PO4" + ] + }, + "RNA-FA Extended": { + "target_nucleotides": ["A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"], + "mapping": ["A->A", "C->C", "G->G", "U->U"], + "can_cross_link": "CGA", + "modifications": [ + "G:+C", + "G:+C-HPO3", + "G:+C-H3PO4", + "G:+C-H2O", + "G:+C2", + "G:+C2-HPO3", + "G:+C2-H2O", + "G:+C2-H3PO4", + "C:+C", + "C:+C-H2O", + "C:+C-HPO3", + "C:+C-H3PO4", + "C:+C2", + "C:+C2-HPO3", + "C:+C2-H2O", + "C:+C2-H3PO4", + "A:+C", + "A:+C-HPO3", + "A:+C-H3PO4", + "A:+C-H2O", + "A:+C2", + "A:+C2-HPO3", + "A:+C2-H2O", + "A:+C2-H3PO4" + ], + "fragment_adducts": [ + "U:C3O;C3O", + "U:C4H4N2O2;U'", + "U:C4H2N2O1;U'-H2O", + "U:C9H13N2O9P1;U", + "U:C9H11N2O8P1;U-H2O", + "U:C9H12N2O6;U-HPO3", + "U:C9H10N2O5;U-H3PO4", + "G:C;FA", + "G:C5H5N5O;G'", + "G:C10H14N5O8P;G", + "G:C6H5N5O;G'+FA", + "G:C11H14N5O8P;G+FA", + "G:C11H12N5O7P;G+FA-H2O", + "G:C11H11N5O4;G+FA-H3PO4", + "G:C11H13N5O5;G+FA-HPO3", + "G:C7H5N5O;G'+2FA", + "G:C12H14N5O8P;G+2FA", + "G:C12H12N5O7P;G+2FA-H2O", + "G:C12H11N5O4;G+2FA-H3PO4", + "G:C12H13N5O5;G+2FA-HPO3", + "C:C;FA", + "C:C4H5N3O;C'", + "C:C9H14N3O8P;C", + "C:C5H5N3O;C'+FA", + "C:C10H14N3O8P;C+FA", + "C:C10H13N3O5;C+FA-HPO3", + "C:C10H12N3O7P;C+FA-H2O", + "C:C10H11N3O4;C+FA-H3PO4", + "C:C6H5N3O;C'+2FA", + "C:C11H14N3O8P;C+2FA", + "C:C11H13N3O5;C+2FA-HPO3", + "C:C11H12N3O7P;C+2FA-H2O", + "C:C11H11N3O4;C+2FA-H3PO4", + "A:C;FA", + "A:C5H5N5;A'", + "A:C10H14N5O7P;A", + "A:C6H5N5;A'+FA", + "A:C11H14N5O7P;A+FA", + "A:C11H13N5O4;A+FA-HPO3", + "A:C11H12N5O6P;A+FA-H2O", + "A:C11H11N5O3;A+FA-H3PO4", + "A:C7H5N5;A'+2FA", + "A:C12H14N5O7P;A+2FA", + "A:C12H13N5O4;A+2FA-HPO3", + "A:C12H12N5O6P;A+2FA-H2O", + "A:C12H11N5O3;A+2FA-H3PO4" + ] + }, + "DNA-FA": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "d->d"], + "can_cross_link": "CGAd", + "modifications": [ + "G:+C", + "G:+C-HPO3", + "G:+C-H3PO4", + "G:+C-H2O", + "C:+C", + "C:+C-H2O", + "C:+C-HPO3", + "C:+C-H3PO4", + "A:+C", + "A:+C-HPO3", + "A:+C-H2O", + "A:+C-H3PO4", + "d:", + "d:-H2O", + "d:-H3PO4", + "d:-HPO3" + ], + "fragment_adducts": [ + "T:C5H6N2O2;T'", + "T:C5H4N2O1;T'-H2O", + "T:C10H15N2O8P1;T", + "T:C10H13N2O7P1;T-H2O", + "T:C10H12N2O4;T-HPO3", + "T:C10H10N2O3;T-H3PO4", + "G:C;FA", + "G:C5H5N5O;G'", + "G:C10H14N5O7P;G", + "G:C6H5N5O;G'+FA", + "G:C11H14N5O7P;G+FA", + "G:C11H13N5O4;G+FA-HPO3", + "G:C11H12N5O6P;G+FA-H2O", + "G:C11H11N5O3;G+FA-H3PO4", + "G:C7H5N5O;G'+2FA", + "G:C12H14N5O7P;G+2FA", + "G:C12H13N5O4;G+2FA-HPO3", + "G:C12H12N5O6P;G+2FA-H2O", + "G:C12H11N5O3;G+2FA-H3PO4", + "C:C;FA", + "C:C4H5N3O;C'", + "C:C9H14N3O7P;C", + "C:C5H5N3O;C'+FA", + "C:C10H14N3O7P;C+FA", + "C:C10H13N3O4;C+FA-HPO3", + "C:C10H12N3O6P;C+FA-H2O", + "C:C10H11N3O3;C+FA-H3PO4", + "C:C6H5N3O;C'+2FA", + "C:C11H14N3O7P;C+2FA", + "C:C11H13N3O4;C+2FA-HPO3", + "C:C11H12N3O6P;C+2FA-H2O", + "C:C11H11N3O3;C+2FA-H3PO4", + "A:C;FA", + "A:C5H5N5;A'", + "A:C10H14N5O6P;A", + "A:C6H5N5;A'+FA", + "A:C11H14N5O6P;A+FA", + "A:C11H13N5O3;A+FA-HPO3", + "A:C11H12N5O5P;A+FA-H2O", + "A:C11H11N5O2;A+FA-H3PO4", + "A:C7H5N5;A'+2FA", + "A:C12H14N5O6P;A+2FA", + "A:C12H13N5O3;A+2FA-HPO3", + "A:C12H12N5O5P;A+2FA-H2O", + "A:C12H11N5O2;A+2FA-H3PO4", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "DNA-FA Extended": { + "target_nucleotides": ["A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"], + "mapping": ["A->A", "C->C", "G->G", "T->T", "d->d"], + "can_cross_link": "CGAd", + "modifications": [ + "G:+C", + "G:+C-HPO3", + "G:+C-H3PO4", + "G:+C-H2O", + "G:+C2", + "G:+C2-HPO3", + "G:+C2-H3PO4", + "G:+C2-H2O", + "C:+C", + "C:+C-H2O", + "C:+C-HPO3", + "C:+C-H3PO4", + "C:+C2", + "C:+C2-HPO3", + "C:+C2-H3PO4", + "C:+C2-H2O", + "A:+C", + "A:+C-HPO3", + "A:+C-H2O", + "A:+C-H3PO4", + "A:+C2", + "A:+C2-HPO3", + "A:+C2-H3PO4", + "A:+C2-H2O", + "d:", + "d:-H2O", + "d:-H3PO4", + "d:-HPO3" + ], + "fragment_adducts": [ + "T:C5H6N2O2;T'", + "T:C5H4N2O1;T'-H2O", + "T:C10H15N2O8P1;T", + "T:C10H13N2O7P1;T-H2O", + "T:C10H12N2O4;T-HPO3", + "T:C10H10N2O3;T-H3PO4", + "G:C;FA", + "G:C5H5N5O;G'", + "G:C10H14N5O7P;G", + "G:C6H5N5O;G'+FA", + "G:C11H14N5O7P;G+FA", + "G:C11H13N5O4;G+FA-HPO3", + "G:C11H12N5O6P;G+FA-H2O", + "G:C11H11N5O3;G+FA-H3PO4", + "G:C7H5N5O;G'+2FA", + "G:C12H14N5O7P;G+2FA", + "G:C12H13N5O4;G+2FA-HPO3", + "G:C12H12N5O6P;G+2FA-H2O", + "G:C12H11N5O3;G+2FA-H3PO4", + "C:C;FA", + "C:C4H5N3O;C'", + "C:C9H14N3O7P;C", + "C:C5H5N3O;C'+FA", + "C:C10H14N3O7P;C+FA", + "C:C10H13N3O4;C+FA-HPO3", + "C:C10H12N3O6P;C+FA-H2O", + "C:C10H11N3O3;C+FA-H3PO4", + "C:C6H5N3O;C'+2FA", + "C:C11H14N3O7P;C+2FA", + "C:C11H13N3O4;C+2FA-HPO3", + "C:C11H12N3O6P;C+2FA-H2O", + "C:C11H11N3O3;C+2FA-H3PO4", + "A:C;FA", + "A:C5H5N5;A'", + "A:C10H14N5O6P;A", + "A:C6H5N5;A'+FA", + "A:C11H14N5O6P;A+FA", + "A:C11H13N5O3;A+FA-HPO3", + "A:C11H12N5O5P;A+FA-H2O", + "A:C11H11N5O2;A+FA-H3PO4", + "A:C7H5N5;A'+2FA", + "A:C12H14N5O6P;A+2FA", + "A:C12H13N5O3;A+2FA-HPO3", + "A:C12H12N5O5P;A+2FA-H2O", + "A:C12H11N5O2;A+2FA-H3PO4", + "d:C5H9O6P;C5H9O6P", + "d:C5H7O5P;C5H9O6P-H2O", + "d:C5H8O3;C5H9O6P-HPO3", + "d:C5H6O2;C5H9O6P-H3PO4" + ] + }, + "none": { + "target_nucleotides": [], + "mapping": [], + "can_cross_link": "", + "modifications": [], + "fragment_adducts": [] + } +} diff --git a/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLPresets.h b/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLPresets.h index de99e36916a..2442bf625b1 100644 --- a/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLPresets.h +++ b/src/openms/include/OpenMS/ANALYSIS/NUXL/NuXLPresets.h @@ -10,6 +10,8 @@ #include #include +#include +#include namespace OpenMS { @@ -17,1510 +19,46 @@ namespace OpenMS // MS1 (modifications) and MS2 (fragments) for the different protocols namespace NuXLPresets { - - static constexpr std::array modifications_RNA_UV - { - "U:", - "U:-H2O", - - "C:", - "C:-H2O", - "C:-NH3", - - "G:", - "G:-H2O", - "G:-NH3", - - "A:", - "A:-NH3" - }; - - static constexpr std::array modifications_RNA_UV_EXTENDED - { - "U:", - "U:-H2O", - "U:-HPO3", - "U:-H3PO4", - "U:-HPO3-C2H3NO", //RBSID - - "C:", - "C:-NH3", - "C:-H2O", - "C:-HPO3", - "C:-H3PO4", - "C:-NH3-H2O", - "C:-NH3-HPO3", - "C:-NH3-H3PO4", - - "G:", - "G:-H2O", - "G:-NH3", - "G:-HPO3", - "G:-H3PO4", - "G:-NH3-H2O", - "G:-NH3-HPO3", - "G:-NH3-H3PO4", - - "A:", - "A:-H2O", - "A:-HPO3", - "A:-H3PO4", - "A:-NH3", - "A:-NH3-H2O", - "A:-NH3-HPO3", - "A:-NH3-H3PO4" - }; - - static constexpr std::array modifications_RNA_UV_4SU - { - "S:", - "S:-H2O", - "S:-H2S", - "S:-C5H8O4", - "S:-C5H8O4-H2O", - "S:-C5H8O4-H2S" - }; - - static constexpr std::array modifications_RNA_UV_4SU_EXTENDED - { - "S:", - "S:-H2O", - "S:-H3PO4", - "S:-HPO3", - "S:-H2S", - "S:+HPO3-H2S", // iTRAPP - "S:-HPO3-H2S", //pRBSID - "S:+HPO3", //iTRAPP - - "S:-C5H8O4", - "S:-C5H8O4-H2O", - "S:-C5H8O4-H3PO4", - "S:-C5H8O4-HPO3", - "S:-C5H8O4-HPO3-H2S", ///pRBSID - "S:-C5H8O4-H2S" - }; - - static constexpr std::array modifications_RNA_UV_6SG - { - "X:", - "X:-H2O", - "X:-H2S", - "X:-C5H8O4", - "X:-C5H8O4-H2O", - "X:-C5H8O4-H2S" - }; - - static constexpr std::array modifications_RNA_UV_6SG_EXTENDED - { - "X:", - "X:-H2O", - "X:-H3PO4", - "X:-HPO3", - "X:-H2S", - "X:-HPO3-H2S", //pRBSID - - - "X:-C5H8O4", - "X:-C5H8O4-H2O", - "X:-C5H8O4-HPO3", - "X:-C5H8O4-HPO3-H2S", ///pRBSID - "X:-C5H8O4-H2S" - }; - - static constexpr std::array modifications_RNA_NM - { - "U:+C5H9N1", - "G:+C5H9N1", - "C:+C5H9N1", - "A:+C5H9N1" - }; - - static constexpr std::array modifications_RNA_NM_EXTENDED - { - "U:+C5H9N1", - "U:+C5H9N1-HPO3", - "U:+C5H9N1-H2O", - "U:+C5H9N1-H3PO4", - "U:+C5H9N1-H2O-H2O", - "U:+C5H9N1-H3PO4-H2O", - - "G:+C5H9N1", - "G:+C5H9N1-HPO3", - "G:+C5H9N1-H2O", - "G:+C5H9N1-H3PO4", - "G:+C5H9N1-H2O-H2O", - "G:+C5H9N1-H3PO4-H2O", - "G:+C5H9N1-NH3", - "G:+C5H9N1-NH3-H2O", - "G:+C5H9N1-NH3-HPO3", - "G:+C5H9N1-NH3-H3PO4", - - "C:+C5H9N1", - "C:+C5H9N1-HPO3", - "C:+C5H9N1-H2O", - "C:+C5H9N1-H3PO4", - "C:+C5H9N1-H2O-H2O", - "C:+C5H9N1-H3PO4-H2O", - "C:+C5H9N1-NH3", - "C:+C5H9N1-NH3-H2O", - "C:+C5H9N1-NH3-HPO3", - "C:+C5H9N1-NH3-H3PO4", - - "A:+C5H9N1", - "A:+C5H9N1-HPO3", - "A:+C5H9N1-H2O", - "A:+C5H9N1-H3PO4", - "A:+C5H9N1-NH3", - "A:+C5H9N1-NH3-H2O", - "A:+C5H9N1-NH3-HPO3", - "A:+C5H9N1-NH3-H3PO4" - }; - - static constexpr std::array modifications_RNA_NM_EXTENDED_H2O - { - "U:+C5H9N1", - "U:+C5H9N1-HPO3", - "U:+C5H9N1-H2O", - "U:+C5H9N1-H3PO4", - "U:+C5H9N1-H2O-H2O", - "U:+C5H9N1-H3PO4-H2O", - - "G:+C5H9N1", - "G:+C5H9N1-HPO3", - "G:+C5H9N1-H2O", - "G:+C5H9N1-H3PO4", - "G:+C5H9N1-H2O-H2O", - "G:+C5H9N1-H3PO4-H2O", - "G:+C5H9N1-NH3", - "G:+C5H9N1-NH3-H2O", - "G:+C5H9N1-NH3-HPO3", - "G:+C5H9N1-NH3-H3PO4", - "G:+C5H9N1+H2O", - - "C:+C5H9N1", - "C:+C5H9N1-HPO3", - "C:+C5H9N1-H2O", - "C:+C5H9N1-H3PO4", - "C:+C5H9N1-H2O-H2O", - "C:+C5H9N1-H3PO4-H2O", - "C:+C5H9N1-NH3", - "C:+C5H9N1-NH3-H2O", - "C:+C5H9N1-NH3-HPO3", - "C:+C5H9N1-NH3-H3PO4", - - "A:+C5H9N1", - "A:+C5H9N1-HPO3", - "A:+C5H9N1-H2O", - "A:+C5H9N1-H3PO4", - "A:+C5H9N1-NH3", - "A:+C5H9N1-NH3-H2O", - "A:+C5H9N1-NH3-HPO3", - "A:+C5H9N1-NH3-H3PO4", - "A:+C5H9N1+H2O" - }; - - static constexpr std::array modifications_RNA_DEB - { - "U:+C4H6O2", - "G:+C4H6O2", - "C:+C4H6O2", - "A:+C4H6O2" - }; - - static constexpr std::array modifications_RNA_DEB_EXTENDED - { - "U:+C4H6O2", - "U:+C4H6O2-H2O", - "U:+C4H6O2-HPO3", - "U:+C4H6O2-H3PO4", - "U:+C4H6O2-H2O-H2O", - "U:+C4H6O2-H3PO4-H2O", - - "G:+C4H6O2", - "G:+C4H6O2-H2O", - "G:+C4H6O2-HPO3", - "G:+C4H6O2-H3PO4", - "G:+C4H6O2-H2O-H2O", - "G:+C4H6O2-H3PO4-H2O", - "G:+C4H6O2-NH3", - "G:+C4H6O2-NH3-H2O", - "G:+C4H602-NH3-HPO3", - "G:+C4H6O2-NH3-H3PO4", - - "C:+C4H6O2", - "C:+C4H6O2-H2O", - "C:+C4H6O2-HPO3", - "C:+C4H6O2-H3PO4", - "C:+C4H6O2-H2O-H2O", - "C:+C4H6O2-H3PO4-H2O", - "C:+C4H6O2-NH3", - "C:+C4H6O2-NH3-H2O", - "C:+C4H602-NH3-HPO3", - "C:+C4H6O2-NH3-H3PO4", - - "A:+C4H6O2", - "A:+C4H6O2-H2O", - "A:+C4H6O2-HPO3", - "A:+C4H6O2-H3PO4", - "A:+C4H6O2-NH3", - "A:+C4H6O2-NH3-H2O", - "A:+C4H6O2-NH3-HPO3", - "A:+C4H6O2-NH3-H3PO4" - }; - - static constexpr std::array modifications_RNA_FA - { - "G:+C", - "G:+C-HPO3", - "G:+C-H3PO4", - "G:+C-H2O", - - "C:+C", - "C:+C-H2O", - "C:+C-HPO3", - "C:+C-H3PO4", - - "A:+C", - "A:+C-HPO3", - "A:+C-H3PO4", - "A:+C-H2O", - }; - - static constexpr std::array modifications_RNA_FA_EXTENDED - { - "G:+C", - "G:+C-HPO3", - "G:+C-H3PO4", - "G:+C-H2O", - "G:+C2", - "G:+C2-HPO3", - "G:+C2-H2O", - "G:+C2-H3PO4", - - "C:+C", - "C:+C-H2O", - "C:+C-HPO3", - "C:+C-H3PO4", - "C:+C2", - "C:+C2-HPO3", - "C:+C2-H2O", - "C:+C2-H3PO4", - - "A:+C", - "A:+C-HPO3", - "A:+C-H3PO4", - "A:+C-H2O", - "A:+C2", - "A:+C2-HPO3", - "A:+C2-H2O", - "A:+C2-H3PO4" - }; - static constexpr std::array modifications_DNA_FA - { - "G:+C", - "G:+C-HPO3", - "G:+C-H3PO4", - "G:+C-H2O", - - "C:+C", - "C:+C-H2O", - "C:+C-HPO3", - "C:+C-H3PO4", - - "A:+C", - "A:+C-HPO3", - "A:+C-H2O", - "A:+C-H3PO4", - - "d:", - "d:-H2O", - "d:-H3PO4", - "d:-HPO3" - }; - - static constexpr std::array modifications_DNA_FA_EXTENDED - { - "G:+C", - "G:+C-HPO3", - "G:+C-H3PO4", - "G:+C-H2O", - "G:+C2", - "G:+C2-HPO3", - "G:+C2-H3PO4", - "G:+C2-H2O", - - "C:+C", - "C:+C-H2O", - "C:+C-HPO3", - "C:+C-H3PO4", - "C:+C2", - "C:+C2-HPO3", - "C:+C2-H3PO4", - "C:+C2-H2O", - - "A:+C", - "A:+C-HPO3", - "A:+C-H2O", - "A:+C-H3PO4", - "A:+C2", - "A:+C2-HPO3", - "A:+C2-H3PO4", - "A:+C2-H2O", - - "d:", - "d:-H2O", - "d:-H3PO4", - "d:-HPO3" - }; - - static constexpr std::array modifications_DNA_UV - { - "T:", - "T:-H2O", - - "G:", - "G:-H2O", - "G:-NH3", - - "A:", - "A:-NH3", - - "C:", - "C:-H2O", - "C:-NH3", - - "d:", // deoxyribosephosphate (d in lower-letter = needs to be the cross-linked nt) - "d:-H2O" - }; - - static constexpr std::array modifications_DNA_UV_EXTENDED - { - "T:", - "T:-H2O", - "T:-H3PO4", - "T:-HPO3", - - "C:", - "C:-H2O", - "C:-H3PO4", - "C:-HPO3", - "C:-NH3", - "C:-NH3-H2O", - "C:-NH3-HPO3", - "C:-NH3-H3PO4", - - "G:", - "G:-H2O", - "G:-H3PO4", - "G:-HPO3", - "G:-NH3", - "G:-NH3-H2O", - "G:-NH3-HPO3", - "G:-NH3-H3PO4", - - "A:", - "A:-NH3", - "A:-H2O", - "A:-H3PO4", - "A:-HPO3", - "A:-NH3-H2O", - "A:-NH3-HPO3", - "A:-NH3-H3PO4", - - "d:", // deoxyribosephosphate (d in lower-letter = needs to be the cross-linked nt) - "d:-H2O", - "d:-H3PO4", - "d:-HPO3" - }; - - static constexpr std::array modifications_DNA_DEB - { - "T:+C4H6O2", - "G:+C4H6O2", - "C:+C4H6O2", - "A:+C4H6O2", - - "d:", // deoxyribosephosphate (d in lower-letter = needs to be the cross-linked nt) - "d:-H2O" - }; - - static constexpr std::array modifications_DNA_DEB_EXTENDED - { - "T:+C4H6O2", - "T:+C4H6O2-H2O", - "T:+C4H6O2-HPO3", - "T:+C4H6O2-H3PO4", - "T:+C4H6O2-H2O-H2O", - "T:+C4H6O2-H3PO4-H2O", - - "G:+C4H6O2", - "G:+C4H6O2-H2O", - "G:+C4H6O2-HPO3", - "G:+C4H6O2-H3PO4", - "G:+C4H6O2-H2O-H2O", - "G:+C4H6O2-H3PO4-H2O", - "G:+C4H6O2-NH3", - "G:+C4H6O2-NH3-H2O", - "G:+C4H6O2-NH3-HPO3", - "G:+C4H6O2-NH3-H3PO4", - - "C:+C4H6O2", - "C:+C4H6O2-H2O", - "C:+C4H6O2-HPO3", - "C:+C4H6O2-H3PO4", - "C:+C4H6O2-H2O-H2O", - "C:+C4H6O2-H3PO4-H2O", - "C:+C4H6O2-NH3-H2O", - "C:+C4H6O2-NH3", - "C:+C4H6O2-NH3-HPO3", - "C:+C4H6O2-NH3-H3PO4", - - "A:+C4H6O2", - "A:+C4H6O2-H2O", - "A:+C4H6O2-H3PO4", - "A:+C4H6O2-HPO3", - "A:+C4H6O2-NH3", - "A:+C4H6O2-NH3-H2O", - "A:+C4H6O2-NH3-HPO3", - "A:+C4H6O2-NH3-H3PO4", - - "d:", // deoxyribosephosphate (d in lower-letter = needs to be the cross-linked nt) - "d:-H2O", - "d:-H3PO4", - "d:-HPO3" - }; - - static constexpr std::array modifications_DNA_NM - { - "T:+C5H9N1", - "G:+C5H9N1", - "C:+C5H9N1", - "A:+C5H9N1", - "d:", - "d:-H2O" - }; - - static constexpr std::array modifications_DNA_NM_EXTENDED - { - "T:+C5H9N1", - "T:+C5H9N1-H2O", - "T:+C5H9N1-HPO3", - "T:+C5H9N1-H3PO4", - "T:+C5H9N1-H2O-H2O", - "T:+C5H9N1-H3PO4-H2O", - - "G:+C5H9N1", - "G:+C5H9N1-H2O", - "G:+C5H9N1-HPO3", - "G:+C5H9N1-H3PO4", - "G:+C5H9N1-H2O-H2O", - "G:+C5H9N1-H3PO4-H2O", - "G:+C5H9N1-NH3", - "G:+C5H9N1-NH3-H2O", - "G:+C5H9N1-NH3-HPO3", - "G:+C5H9N1-NH3-H3PO4", - - "C:+C5H9N1", - "C:+C5H9N1-H2O", - "C:+C5H9N1-HPO3", - "C:+C5H9N1-H3PO4", - "C:+C5H9N1-H2O-H2O", - "C:+C5H9N1-H3PO4-H2O", - "C:+C5H9N1-NH3", - "C:+C5H9N1-NH3-HPO3", - "C:+C5H9N1-NH3-H2O", - "C:+C5H9N1-NH3-H3PO4", - - "A:+C5H9N1", - "A:+C5H9N1-HPO3", - "A:+C5H9N1-H2O", - "A:+C5H9N1-H3PO4", - "A:+C5H9N1-NH3", - "A:+C5H9N1-NH3-HPO3", - "A:+C5H9N1-NH3-H2O", - "A:+C5H9N1-NH3-H3PO4", - - "d:", - "d:-H2O", - "d:-H3PO4", - "d:-HPO3" - }; - - static constexpr std::array modifications_DNA_BrU_UV - { - "T:", - "T:-H2O", - - "B:", - "B:-H2O", - - "G:", - "G:-H2O", - "G:-NH3", - - "A:", - "A:-NH3", - - "C:", - "C:-H2O", - "C:-NH3", - - "d:", // deoxyribosephosphate (d in lower-letter = needs to be the cross-linked nt) - "d:-H2O" - }; - - - /////////////////////////////////////////////////////////////////////////////////// - // fragment definitions - /////////////////////////////////////////////////////////////////////////////////// - - // shared by default and Extended - static constexpr std::array fragments_RNA_UV - { - "U:C3O;C3O", - "U:C4H4N2O2;U'", - "U:C4H2N2O1;U'-H2O", - "U:C9H13N2O9P1;U", - "U:C9H11N2O8P1;U-H2O", - "U:C9H12N2O6;U-HPO3", - "U:C9H10N2O5;U-H3PO4", - - "C:C4H5N3O;C'", - "C:C4H3N3;C'-H2O", - "C:C4H2N2O;C'-NH3", - "C:C9H14N3O8P;C", - "C:C9H11N2O8P;C-NH3", - "C:C9H12N3O7P;C-H2O", - "C:C9H9N2O7P;C-NH3-H2O", - "C:C9H13N3O5;C-HPO3", - "C:C9H11N3O4;C-H3PO4", - "C:C9H10N2O5;C-NH3-HPO3", - "C:C9H8N2O4;C-NH3-H3PO4", - - - "G:C5H5N5O;G'", - "G:C5H3N5;G'-H2O", - "G:C5H2N4O;G'-NH3", - "G:C10H14N5O8P;G", - "G:C10H12N5O7P;G-H2O", - "G:C10H11N4O8P;G-NH3", - "G:C10H9N4O7P;G-NH3-H2O", - "G:C10H13N5O5;G-HPO3", - "G:C10H11N5O4;G-H3PO4", - "G:C10H10N4O5;G-NH3-HPO3", - "G:C10H8N4O4;G-NH3-H3PO4", - - "A:C5H5N5;A'", - "A:C5H2N4;A'-NH3", - "A:C10H14N5O7P;A", - "A:C10H12N5O6P;A-H2O", - "A:C10H11N4O7P;A-NH3", - "A:C10H9N4O6P;A-NH3-H2O", - "A:C10H13N5O4;A-HPO3", - "A:C10H11N5O3;A-H3PO4", - "A:C10H10N5O4;A-NH3-HPO3", - "A:C10H8N5O3;A-NH3-H3PO4" - }; - - // shared by default and Extended - static constexpr std::array fragments_RNA_UV_4SU - { - "S:C9H10N2O5;tU-H2S", // 4SU - H2S - "S:C4H2N2O1;tU'-H2S", // 4SU base - H2S - - "U:C3O;C3O", - "U:C4H4N2O2;U'", - "U:C4H2N2O1;U'-H2O", - "U:C9H13N2O9P1;U", - "U:C9H11N2O8P1;U-H2O", - "U:C9H12N2O6;U-HPO3", - "U:C9H10N2O5;U-H3PO4", - - "C:C4H5N3O;C'", - "C:C4H3N3;C'-H2O", - "C:C4H2N2O;C'-NH3", - "C:C9H14N3O8P;C", - "C:C9H11N2O8P;C-NH3", - "C:C9H12N3O7P;C-H2O", - "C:C9H9N2O7P;C-NH3-H2O", - "C:C9H13N3O5;C-HPO3", - "C:C9H11N3O4;C-H3PO4", - "C:C9H10N2O5;C-NH3-HPO3", - "C:C9H8N2O4;C-NH3-H3PO4", - - "G:C5H5N5O;G'", - "G:C5H3N5;G'-H2O", - "G:C5H2N4O;G'-NH3", - "G:C10H14N5O8P;G", - "G:C10H12N5O7P;G-H2O", - "G:C10H11N4O8P;G-NH3", - "G:C10H9N4O7P;G-NH3-H2O", - "G:C10H13N5O5;G-HPO3", - "G:C10H11N5O4;G-H3PO4", - "G:C10H10N4O5;G-NH3-HPO3", - "G:C10H8N4O4;G-NH3-H3PO4", - - "A:C5H5N5;A'", - "A:C5H2N4;A'-NH3", - "A:C10H14N5O7P;A", - "A:C10H12N5O6P;A-H2O", - "A:C10H11N4O7P;A-NH3", - "A:C10H9N4O6P;A-NH3-H2O", - "A:C10H13N5O4;A-HPO3", - "A:C10H11N5O3;A-H3PO4", - "A:C10H10N5O4;A-NH3-HPO3", - "A:C10H8N5O3;A-NH3-H3PO4" - }; - - static constexpr std::array fragments_RNA_UV_6SG - { - "X:C10H11N5O4;tG-H2S", - "X:C5H3N5;tG'-H2S", - - "U:C3O;C3O", - "U:C4H4N2O2;U'", - "U:C4H2N2O1;U'-H2O", - "U:C9H13N2O9P1;U", - "U:C9H11N2O8P1;U-H2O", - "U:C9H12N2O6;U-HPO3", - "U:C9H10N2O5;U-H3PO4", - - "C:C4H5N3O;C'", - "C:C4H3N3;C'-H2O", - "C:C4H2N2O;C'-NH3", - "C:C9H14N3O8P;C", - "C:C9H11N2O8P;C-NH3", - "C:C9H12N3O7P;C-H2O", - "C:C9H9N2O7P;C-NH3-H2O", - "C:C9H13N3O5;C-HPO3", - "C:C9H11N3O4;C-H3PO4", - "C:C9H10N2O5;C-NH3-HPO3", - "C:C9H8N2O4;C-NH3-H3PO4", - - "G:C5H5N5O;G'", - "G:C5H3N5;G'-H2O", - "G:C5H2N4O;G'-NH3", - "G:C10H14N5O8P;G", - "G:C10H12N5O7P;G-H2O", - "G:C10H11N4O8P;G-NH3", - "G:C10H9N4O7P;G-NH3-H2O", - "G:C10H13N5O5;G-HPO3", - "G:C10H11N5O4;G-H3PO4", - "G:C10H10N4O5;G-NH3-HPO3", - "G:C10H8N4O4;G-NH3-H3PO4", - - "A:C5H5N5;A'", - "A:C5H2N4;A'-NH3", - "A:C10H14N5O7P;A", - "A:C10H12N5O6P;A-H2O", - "A:C10H11N4O7P;A-NH3", - "A:C10H9N4O6P;A-NH3-H2O", - "A:C10H13N5O4;A-HPO3", - "A:C10H11N5O3;A-H3PO4", - "A:C10H10N5O4;A-NH3-HPO3", - "A:C10H8N5O3;A-NH3-H3PO4" - }; - - // shared by default and Extended - static constexpr std::array fragments_DNA_UV - { - "T:C5H6N2O2;T'", - "T:C5H4N2O;T'-H2O", - "T:C10H15N2O8P;T", - "T:C10H13N2O7P;T-H2O", - "T:C10H14N2O5;T-HPO3", - "T:C10H12N2O4;T-H3PO4", - - "C:C9H14N3O7P;C", - "C:C9H11N2O7P;C-NH3", - "C:C9H12N3O6P;C-H2O", - "C:C9H9N2O6P;C-NH3-H2O", - "C:C9H13N3O4;C-HPO3", - "C:C9H11N3O3;C-H3PO4", - "C:C9H10N2O4;C-NH3-HPO3", - "C:C9H8N2O3;C-NH3-H3PO4", - "C:C4H5N3O;C'", - "C:C4H3N3;C'-H2O", - "C:C4H2N2O;C'-NH3", - - "G:C10H14N5O7P;G", - "G:C10H12N5O6P;G-H2O", - "G:C10H11N4O7P;G-NH3", - "G:C10H9N4O6P;G-NH3-H2O", - "G:C10H13N5O4;G-HPO3", - "G:C10H10N4O4;G-NH3-HPO3", - "G:C10H11N5O3;G-H3PO4", - "G:C10H8N4O3;G-NH3-H3PO4", - "G:C5H5N5O;G'", - "G:C5H3N5;G'-H2O", - "G:C5H2N4O;G'-NH3", - - "A:C10H14N5O6P;A", - "A:C10H12N5O5P;A-H2O", - "A:C10H11N4O6P;A-NH3", - "A:C10H9N4O5P;A-NH3-H2O", - "A:C10H13N5O3;A-HPO3", - "A:C10H11N5O2;A-H3PO4", - "A:C10H10N5O3;A-NH3-HPO3", - "A:C10H8N5O2;A-NH3-H3PO4", - "A:C5H5N5;A'", - "A:C5H2N4;A'-NH3", - - // base was lost -> only dribose = C5H9O6P remains - "d:C5H9O6P;C5H9O6P", - "d:C5H7O5P;C5H9O6P-H2O", - "d:C5H8O3;C5H9O6P-HPO3", - "d:C5H6O2;C5H9O6P-H3PO4" - }; - - // shared by default and Extended - static constexpr std::array fragments_DNA_BrU_UV - { - "T:C5H6N2O2;T'", - "T:C5H4N2O;T'-H2O", - "T:C10H15N2O8P;T", - "T:C10H13N2O7P;T-H2O", - "T:C10H14N2O5;T-HPO3", - "T:C10H12N2O4;T-H3PO4", - - "B:C4H2N2O2;B'", - "B:C4N2O;B'-H2O", - "B:C9H11N2O8P;B", - "B:C9H9N2O7P;B-H2O", - "B:C9H10N2O5;B-HPO3", - "B:C9H8N2O4;B-H3PO4", - - "C:C9H14N3O7P;C", - "C:C9H11N2O7P;C-NH3", - "C:C9H12N3O6P;C-H2O", - "C:C9H9N2O6P;C-NH3-H2O", - "C:C9H13N3O4;C-HPO3", - "C:C9H11N3O3;C-H3PO4", - "C:C9H10N2O4;C-NH3-HPO3", - "C:C9H8N2O3;C-NH3-H3PO4", - "C:C4H5N3O;C'", - "C:C4H3N3;C'-H2O", - "C:C4H2N2O;C'-NH3", - - "G:C10H14N5O7P;G", - "G:C10H12N5O6P;G-H2O", - "G:C10H11N4O7P;G-NH3", - "G:C10H9N4O6P;G-NH3-H2O", - "G:C10H13N5O4;G-HPO3", - "G:C10H10N4O4;G-NH3-HPO3", - "G:C10H11N5O3;G-H3PO4", - "G:C10H8N4O3;G-NH3-H3PO4", - "G:C5H5N5O;G'", - "G:C5H3N5;G'-H2O", - "G:C5H2N4O;G'-NH3", - - "A:C10H14N5O6P;A", - "A:C10H12N5O5P;A-H2O", - "A:C10H11N4O6P;A-NH3", - "A:C10H9N4O5P;A-NH3-H2O", - "A:C10H13N5O3;A-HPO3", - "A:C10H11N5O2;A-H3PO4", - "A:C10H10N5O3;A-NH3-HPO3", - "A:C10H8N5O2;A-NH3-H3PO4", - "A:C5H5N5;A'", - "A:C5H2N4;A'-NH3", - - // base was lost -> only dribose = C5H9O6P remains - "d:C5H9O6P;C5H9O6P", - "d:C5H7O5P;C5H9O6P-H2O", - "d:C5H8O3;C5H9O6P-HPO3", - "d:C5H6O2;C5H9O6P-H3PO4" - }; - - // shared by default and Extended - static constexpr std::array fragments_RNA_DEB - { - "U:C4H6O2;DEB", - "U:C4H4O;DEB-H2O", - "U:C7H6O3;DEB+C3O", - "U:C8H10N2O4;DEB+U'", - "U:C8H8N2O3;DEB+U'-H2O", - "U:C13H19N2O11P1;DEB+U", - "U:C13H17N2O10P1;DEB+U-H2O", - "U:C13H18N2O8;DEB+U-HPO3", - "U:C13H16N2O7;DEB+U-H3PO4", - - "G:C4H6O2;DEB", - "G:C4H4O;DEB-H2O", - "G:C9H11N5O3;DEB+G'", - "G:C8H9N5O3;DEB+G'-H2O", - "G:C9H8N4O3;DEB+G'-NH3", - "G:C14H20N5O10P1;DEB+G", - "G:C14H18N5O9P1;DEB+G-H2O", - "G:C14H17N4O10P1;DEB+G-NH3", - "G:C14H19N5O7;DEB+G-HPO3", - "G:C14H17N5O6;DEB+G-H3PO4", - "G:C14H16N4O7;DEB+G-NH3-HPO3", - "G:C14H14N4O6;DEB+G-NH3-H3PO4", - "G:C14H15N4O9P1;DEB+G-NH3-H2O", - - "C:C4H6O2;DEB", - "C:C4H4O;DEB-H2O", - "C:C8H11N3O3;DEB+C'", - "C:C8H9N3O2;DEB+C'-H2O", - "C:C8H8N2O3;DEB+C'-NH3", - "C:C13H20N3O10P1;DEB+C", - "C:C13H18N3O9P1;DEB+C-H2O", - "C:C13H17N2O10P1;DEB+C-NH3", - "C:C13H19N3O7;DEB+C-HPO3", - "C:C13H17N3O6;DEB+C-H3PO4", - "C:C13H16N2O7;DEB+C-NH3-HPO3", - "C:C13H14N2O6;DEB+C-NH3-H3PO4", - "C:C13H15N2O9P1;DEB+C-NH3-H2O", - - "A:C4H6O2;DEB", - "A:C4H4O;DEB-H2O", - "A:C9H11N5O2;DEB+A'", - "A:C9H17N4O;DEB+A'-NH3", - "A:C14H20N5O9P1;DEB+A", - "A:C14H18N5O8P1;DEB+A-H2O", - "A:C14H17N4O9P1;DEB+A-NH3", - "A:C14H19N5O6;DEB+A-HPO3", - "A:C14H17N5O5;DEB+A-H3PO4", - "A:C14H16N4O6;DEB+A-NH3-HPO3", - "A:C14H14N4O5;DEB+A-NH3-H3PO4", - "A:C14H15N4O8P1;DEB+A-NH3-H2O" - }; - - // shared by default and Extended - static constexpr std::array fragments_DNA_DEB - { - "T:C4H6O2;DEB", - "T:C4H4O;DEB-H2O", - "T:C9H12N2O4;DEB+T'", - "T:C9H10N2O3;DEB+T'-H2O", - "T:C14H21N2O10P1;DEB+T", - "T:C14H19N2O9P1;DEB+T-H2O", - "T:C14H20N2O7;DEB+T-HPO3", - "T:C14H18N2O6;DEB+T-H3PO4", - - "C:C4H6O2;DEB", - "C:C4H4O;DEB-H2O", - "C:C8H11N3O3;DEB+C'", - "C:C8H8N2O3;DEB+C'-NH3", - "C:C8H9N3O2;DEB+C'-H2O", - "C:C13H20N3O9P1;DEB+C", - "C:C13H17N2O9P1;DEB+C-NH3", - "C:C13H18N3O8P1;DEB+C-H2O", - "C:C13H19N3O6;DEB+C-HPO3", - "C:C13H17N3O5;DEB+C-H3PO4", - "C:C13H16N2O6;DEB+C-NH3-HPO3", - "C:C13H14N2O5;DEB+C-NH3-H3PO4", - "C:C13H15N2O8P1;DEB+C-NH3-H2O", - - "G:C4H6O2;DEB", - "G:C4H4O;DEB-H2O", - "G:C9H11N5O3;DEB+G'", - "G:C9H8N4O3;DEB+G'-NH3", - "G:C9H9N5O2;DEB+G'-H2O", - "G:C14H20N5O9P1;DEB+G", - "G:C14H17N4O9P1;DEB+G-NH3", - "G:C14H18N5O8P1;DEB+G-H2O", - "G:C14H19N5O6;DEB+G-HPO3", - "G:C14H17N5O5;DEB+G-H3PO4", - "G:C14H16N4O6;DEB+G-NH3-HPO3", - "G:C14H14N4O5;DEB+G-NH3-H3PO4", - "G:C14H15N4O8P1;DEB+G-NH3-H2O", - - "A:C4H6O2;DEB", - "A:C4H4O;DEB-H2O", - "A:C9H11N5O2;DEB+A'", - "A:C9H8N4O2;DEB+A'-NH3", - "A:C14H20N5O8P1;DEB+A", - "A:C14H17N4O8P1;DEB+A-NH3", - "A:C14H18N5O7P1;DEB+A-H2O", - "A:C14H19N5O5;DEB+A-HPO3", - "A:C14H17N5O4;DEB+A-H3PO4", - "A:C14H16N4O5;DEB+A-NH3-HPO3", - "A:C14H14N4O4;DEB+A-NH3-H3PO4", - "A:C14H15N4O7P1;DEB+A-NH3-H2O", - - "d:C5H9O6P;C5H9O6P", - "d:C5H7O5P;C5H9O6P-H2O", - "d:C5H8O3;C5H9O6P-HPO3", - "d:C5H6O2;C5H9O6P-H3PO4" - }; - - // shared by default and Extended - static constexpr std::array fragments_RNA_NM - { - "U:C5H9N1;NM", - "U:C8H9N1O1;NM+C3O", - "U:C14H22N3O9P1;NM+U", - "U:C14H20N3O8P1;NM+U-H2O", - "U:C14H21N3O6;NM+U-HPO3", - "U:C14H19N3O5;NM+U-H3PO4", - "U:C9H13N3O2;NM+U'", - "U:C9H11N3O1;NM+U'-H2O", - - "C:C5H9N1;NM", - "C:C14H23N4O8P1;NM+C", - "C:C14H21N4O7P1;NM+C-H2O", - "C:C14H20N3O8P1;NM+C-NH3", - "C:C14H22N4O5;NM+C-HPO3", - "C:C14H20N4O4;NM+C-H3PO4", - "C:C14H19N3O5;NM+C-NH3-HPO3", - "C:C14H17N3O4;NM+C-NH3-H3PO4", - "C:C9H14N4O1;NM+C'", - "C:C9H12N4;NM+C'-H2O", - "C:C9H11N3O1;NM+C'-NH3", - "C:C14H18N3O7P1;NM+C-NH3-H2O", - - "G:C5H9N1;NM", - "G:C15H23N6O8P1;NM+G", - "G:C15H21N6O7P1;NM+G-H2O", - "G:C15H20N5O8P1;NM+G-NH3", - "G:C15H22N6O5;NM+G-HPO3", - "G:C15H20N6O4;NM+G-H3PO4", - "G:C15H19N5O5;NM+G-NH3-HPO3", - "G:C15H17N5O4;NM+G-NH3-H3PO4", - "G:C10H14N6O1;NM+G'", - "G:C10H12N6;NM+G'-H2O", - "G:C10H14N6O1;NM+G'-NH3", - "G:C15H18N5O7P1;NM+G-NH3-H2O", - - "A:C5H9N1;NM", - "A:C15H23N6O7P1;NM+A", - "A:C15H21N6O6P1;NM+A-H2O", - "A:C15H20N5O7P1;NM+A-NH3", - "A:C15H22N6O4;NM+A-HPO3", - "A:C15H20N6O3;NM+A-H3PO4", - "A:C15H19N5O4;NM+A-NH3-HPO3", - "A:C15H17N5O3;NM+A-NH3-H3PO4", - "A:C10H14N6;NM+A'", - "A:C10H11N5;NM+A'-NH3", - "A:C15H18N5O6P1;NM+A-NH3-H2O" - }; - - // +H2O - static constexpr std::array fragments_RNA_NM_H2O - { - "U:C5H9N1;NM", - "U:C8H9N1O1;NM+C3O", - "U:C14H22N3O9P1;NM+U", - "U:C14H20N3O8P1;NM+U-H2O", - "U:C14H21N3O6;NM+U-HPO3", - "U:C14H19N3O5;NM+U-H3PO4", - "U:C9H13N3O2;NM+U'", - "U:C9H11N3O1;NM+U'-H2O", - - "C:C5H9N1;NM", - "C:C14H23N4O8P1;NM+C", - "C:C14H21N4O7P1;NM+C-H2O", - "C:C14H20N3O8P1;NM+C-NH3", - "C:C14H22N4O5;NM+C-HPO3", - "C:C14H20N4O4;NM+C-H3PO4", - "C:C14H19N3O5;NM+C-NH3-HPO3", - "C:C14H17N3O4;NM+C-NH3-H3PO4", - "C:C9H14N4O1;NM+C'", - "C:C9H12N4;NM+C'-H2O", - "C:C9H11N3O1;NM+C'-NH3", - "C:C14H18N3O7P1;NM+C-NH3-H2O", - - "G:C5H9N1;NM", - "G:C15H23N6O8P1;NM+G", - "G:C15H21N6O7P1;NM+G-H2O", - "G:C15H25N6O9P1;NM+G+H2O", - "G:C15H20N5O8P1;NM+G-NH3", - "G:C15H22N6O5;NM+G-HPO3", - "G:C15H20N6O4;NM+G-H3PO4", - "G:C15H19N5O5;NM+G-NH3-HPO3", - "G:C15H17N5O4;NM+G-NH3-H3PO4", - "G:C10H14N6O1;NM+G'", - "G:C10H12N6;NM+G'-H2O", - "G:C10H16N6O2;NM+G'+H2O", - "G:C10H14N6O1;NM+G'-NH3", - "G:C15H18N5O7P1;NM+G-NH3-H2O", - - "A:C5H9N1;NM", - "A:C15H23N6O7P1;NM+A", - "A:C15H21N6O6P1;NM+A-H2O", - "A:C15H25N6O8P1;NM+A+H2O", - "A:C15H20N5O7P1;NM+A-NH3", - "A:C15H22N6O4;NM+A-HPO3", - "A:C15H20N6O3;NM+A-H3PO4", - "A:C15H19N5O4;NM+A-NH3-HPO3", - "A:C15H17N5O3;NM+A-NH3-H3PO4", - "A:C10H14N6;NM+A'", - "A:C10H11N5;NM+A'-NH3", - "A:C10H16N6O;NM+A'+H2O", - "A:C15H18N5O6P1;NM+A-NH3-H2O" - }; - - - static constexpr std::array fragments_RNA_FA - { - "U:C3O;C3O", - "U:C4H4N2O2;U'", - "U:C4H2N2O1;U'-H2O", - "U:C9H13N2O9P1;U", - "U:C9H11N2O8P1;U-H2O", - "U:C9H12N2O6;U-HPO3", - "U:C9H10N2O5;U-H3PO4", - - "G:C;FA", - "G:C5H5N5O;G'", - "G:C10H14N5O8P;G", - "G:C6H5N5O;G'+FA", - "G:C11H14N5O8P;G+FA", - "G:C11H12N5O7P;G+FA-H2O", - "G:C11H11N5O4;G+FA-H3PO4", - "G:C11H13N5O5;G+FA-HPO3", - "G:C7H5N5O;G'+2FA", - "G:C12H14N5O8P;G+2FA", - "G:C12H12N5O7P;G+2FA-H2O", - "G:C12H11N5O4;G+2FA-H3PO4", - "G:C12H13N5O5;G+2FA-HPO3", - - "C:C;FA", - "C:C4H5N3O;C'", - "C:C9H14N3O8P;C", - "C:C5H5N3O;C'+FA", - "C:C10H14N3O8P;C+FA", - "C:C10H13N3O5;C+FA-HPO3", - "C:C10H12N3O7P;C+FA-H2O", - "C:C10H11N3O4;C+FA-H3PO4", - "C:C6H5N3O;C'+2FA", - "C:C11H14N3O8P;C+2FA", - "C:C11H13N3O5;C+2FA-HPO3", - "C:C11H12N3O7P;C+2FA-H2O", - "C:C11H11N3O4;C+2FA-H3PO4", - - "A:C;FA", - "A:C5H5N5;A'", - "A:C10H14N5O7P;A", - "A:C6H5N5;A'+FA", - "A:C11H14N5O7P;A+FA", - "A:C11H13N5O4;A+FA-HPO3", - "A:C11H12N5O6P;A+FA-H2O", - "A:C11H11N5O3;A+FA-H3PO4", - "A:C7H5N5;A'+2FA", - "A:C12H14N5O7P;A+2FA", - "A:C12H13N5O4;A+2FA-HPO3", - "A:C12H12N5O6P;A+2FA-H2O", - "A:C12H11N5O3;A+2FA-H3PO4" - }; - - static constexpr std::array fragments_DNA_FA - { - "T:C5H6N2O2;T'", - "T:C5H4N2O1;T'-H2O", - "T:C10H15N2O8P1;T", - "T:C10H13N2O7P1;T-H2O", - "T:C10H12N2O4;T-HPO3", - "T:C10H10N2O3;T-H3PO4", - - "G:C;FA", - "G:C5H5N5O;G'", - "G:C10H14N5O7P;G", - "G:C6H5N5O;G'+FA", - "G:C11H14N5O7P;G+FA", - "G:C11H13N5O4;G+FA-HPO3", - "G:C11H12N5O6P;G+FA-H2O", - "G:C11H11N5O3;G+FA-H3PO4", - "G:C7H5N5O;G'+2FA", - "G:C12H14N5O7P;G+2FA", - "G:C12H13N5O4;G+2FA-HPO3", - "G:C12H12N5O6P;G+2FA-H2O", - "G:C12H11N5O3;G+2FA-H3PO4", - - "C:C;FA", - "C:C4H5N3O;C'", - "C:C9H14N3O7P;C", - "C:C5H5N3O;C'+FA", - "C:C10H14N3O7P;C+FA", - "C:C10H13N3O4;C+FA-HPO3", - "C:C10H12N3O6P;C+FA-H2O", - "C:C10H11N3O3;C+FA-H3PO4", - "C:C6H5N3O;C'+2FA", - "C:C11H14N3O7P;C+2FA", - "C:C11H13N3O4;C+2FA-HPO3", - "C:C11H12N3O6P;C+2FA-H2O", - "C:C11H11N3O3;C+2FA-H3PO4", - - "A:C;FA", - "A:C5H5N5;A'", - "A:C10H14N5O6P;A", - "A:C6H5N5;A'+FA", - "A:C11H14N5O6P;A+FA", - "A:C11H13N5O3;A+FA-HPO3", - "A:C11H12N5O5P;A+FA-H2O", - "A:C11H11N5O2;A+FA-H3PO4", - "A:C7H5N5;A'+2FA", - "A:C12H14N5O6P;A+2FA", - "A:C12H13N5O3;A+2FA-HPO3", - "A:C12H12N5O5P;A+2FA-H2O", - "A:C12H11N5O2;A+2FA-H3PO4", - - "d:C5H9O6P;C5H9O6P", - "d:C5H7O5P;C5H9O6P-H2O", - "d:C5H8O3;C5H9O6P-HPO3", - "d:C5H6O2;C5H9O6P-H3PO4" - }; - - // shared by default and Extended - static constexpr std::array fragments_DNA_NM - { - "T:C5H9N1;NM", - "T:C15H24N3O8P1;NM+T", - "T:C15H22N3O7P1;NM+T-H2O", - "T:C15H23N3O5;NM+T-HPO3", - "T:C15H21N3O4;NM+T-H3PO4", - "T:C10H15N3O2;NM+T'", - "T:C10H13N3O1;NM+T'-H2O", - - "C:C5H9N;NM", - "C:C9H14N4O1;NM+C'", - "C:C9H11N3O1;NM+C'-NH3", - "C:C9H12N4;NM+C'-H2O", - "C:C14H23N4O7P1;NM+C", - "C:C14H21N4O6P1;NM+C-H2O", - "C:C14H20N3O7P1;NM+C-NH3", - "C:C14H18N3O6P1;NM+C-NH3-H2O", - "C:C14H20N4O3;NM+C-H3PO4", - "C:C14H22N4O4;NM+C-HPO3", - "C:C14H19N3O4;NM+C-NH3-HPO3", - "C:C14H17N3O3;NM+C-NH3-H3PO4", - - "G:C5H9N1;NM", - "G:C10H14N6O1;NM+G'", - "G:C10H12N6;NM+G'-H2O", - "G:C10H11N5O1;NM+G'-NH3", - "G:C15H23N6O7P1;NM+G", - "G:C15H21N6O6P1;NM+G-H2O", - "G:C15H22N6O4;NM+G-HPO3", - "G:C15H20N6O3;NM+G-H3PO4", - "G:C15H20N5O7P1;NM+G-NH3", - "G:C15H18N5O6P1;NM+G-NH3-H2O", - "G:C15H19N5O4;NM+G-NH3-HPO3", - "G:C15H17N5O3;NM+G-NH3-H3PO4", - - "A:C5H9N1;NM", - "A:C10H14N6;NM+A'", - "A:C10H11N5;NM+A'-NH3", - "A:C15H23N6O6P1;NM+A", - "A:C15H20N6O2;NM+A-H3PO4", - "A:C15H21N6O5P1;NM+A-H2O", - "A:C15H22N6O3;NM+A-HPO3", - "A:C15H20N5O6P1;NM+A-NH3", - "A:C15H18N5O5P1;NM+A-NH3-H2O", - "A:C15H19N5O3;NM+A-NH3-HPO3", - "A:C15H17N5O2;NM+A-NH3-H3PO4", - - "d:C5H9O6P;C5H9O6P", - "d:C5H7O5P;C5H9O6P-H2O", - "d:C5H8O3;C5H9O6P-HPO3", - "d:C5H6O2;C5H9O6P-H3PO4" - }; - - // the nucleotides (=mono-phosphates) and the deoxyribosephosphate (for DNA) - static constexpr std::array DNA_nucleotides {"A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"}; - static constexpr std::array RNA_nucleotides {"A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"}; - static constexpr std::array DNA_mapping {"A->A", "C->C", "G->G", "T->T", "d->d"}; - static constexpr std::array RNA_mapping {"A->A", "C->C", "G->G", "U->U"}; - - static constexpr std::array presets_names { - "none", - "RNA-UV (U)", - "RNA-UV (UCGA)", - "RNA-UV Extended (U)", - "RNA-UV Extended (UCGA)", - "RNA-UV (4SU)", - "RNA-UV Extended (4SU)", - "RNA-UV (6SG)", - "RNA-UV Extended (6SG)", - "RNA-DEB", - "RNA-DEB Extended", - "RNA-NM", - "RNA-NM Extended", - "RNA-NM Extended (+H2O)", - "DNA-UV", - "DNA-UV Extended", - "DNA-DEB", - "DNA-DEB Extended", - "DNA-NM", - "DNA-NM Extended", - "RNA-FA", - "RNA-FA Extended", - "DNA-FA", - "DNA-FA Extended", - "DNA-UV (BrU)" - }; - - void getPresets(const String& p, + /** + @brief Get all available presets names from JSON file + @param custom_presets_file Optional path to a custom presets file + @return StringList containing all available preset names + */ + OPENMS_DLLAPI StringList getAllPresetsNames(const String& custom_presets_file = ""); + + /** + @brief Get preset parameters for a given preset name + @param p The preset name + @param custom_presets_file Optional path to a custom presets file + @param nucleotides Output parameter for nucleotides + @param mapping Output parameter for mapping + @param modifications Output parameter for modifications + @param fragment_adducts Output parameter for fragment adducts + @param can_cross_link Output parameter for can_cross_link + */ + OPENMS_DLLAPI void getPresets(const String& p, + const String& custom_presets_file, StringList& nucleotides, StringList& mapping, StringList& modifications, StringList& fragment_adducts, - String& can_cross_link) - { - // construct name list from constexpr array - const StringList names(presets_names.begin(), presets_names.end()); - - // sanity check: preset name needs to be in the list of supported presets - if (auto it = find(names.begin(), names.end(), p); it == names.end()) - { - throw std::runtime_error("Error: unknown preset."); - } - - // set NTs for RNA / DNA - if (p.hasPrefix("RNA")) - { - nucleotides = StringList(RNA_nucleotides.begin(), RNA_nucleotides.end()); - mapping = StringList(RNA_mapping.begin(), RNA_mapping.end()); - } - else if (p.hasPrefix("DNA")) - { - nucleotides = StringList(DNA_nucleotides.begin(), DNA_nucleotides.end()); - mapping = StringList(DNA_mapping.begin(), DNA_mapping.end()); - } - - // initialize all StringLists from constexpr arrays - // note: we do this here as this raises a logic error if e.g., size of the array doesn't match the reserved size. - // This can easily happen if a comma is omitted and two string literals on two lines joined - StringList RNA_UV_modifications(modifications_RNA_UV.begin(), modifications_RNA_UV.end()); - StringList RNA_UV_EXTENDED_modifications(modifications_RNA_UV_EXTENDED.begin(), modifications_RNA_UV_EXTENDED.end()); - StringList RNA_UV_fragments(fragments_RNA_UV.begin(), fragments_RNA_UV.end()); - - StringList RNA_UV_4SU_modifications(modifications_RNA_UV_4SU.begin(), modifications_RNA_UV_4SU.end()); - StringList RNA_UV_4SU_EXTENDED_modifications(modifications_RNA_UV_4SU_EXTENDED.begin(), modifications_RNA_UV_4SU_EXTENDED.end()); - StringList RNA_UV_4SU_fragments(fragments_RNA_UV_4SU.begin(), fragments_RNA_UV_4SU.end()); - - StringList RNA_UV_6SG_modifications(modifications_RNA_UV_6SG.begin(), modifications_RNA_UV_6SG.end()); - StringList RNA_UV_6SG_EXTENDED_modifications(modifications_RNA_UV_6SG_EXTENDED.begin(), modifications_RNA_UV_6SG_EXTENDED.end()); - StringList RNA_UV_6SG_fragments(fragments_RNA_UV_6SG.begin(), fragments_RNA_UV_6SG.end()); - - StringList DNA_UV_modifications(modifications_DNA_UV.begin(), modifications_DNA_UV.end()); - StringList DNA_UV_EXTENDED_modifications(modifications_DNA_UV_EXTENDED.begin(), modifications_DNA_UV_EXTENDED.end()); - StringList DNA_UV_fragments(fragments_DNA_UV.begin(), fragments_DNA_UV.end()); - - StringList RNA_DEB_modifications(modifications_RNA_DEB.begin(), modifications_RNA_DEB.end()); - StringList RNA_DEB_EXTENDED_modifications(modifications_RNA_DEB_EXTENDED.begin(), modifications_RNA_DEB_EXTENDED.end()); - StringList RNA_DEB_fragments(fragments_RNA_DEB.begin(), fragments_RNA_DEB.end()); - - StringList RNA_NM_modifications(modifications_RNA_NM.begin(), modifications_RNA_NM.end()); - StringList RNA_NM_EXTENDED_modifications(modifications_RNA_NM_EXTENDED.begin(), modifications_RNA_NM_EXTENDED.end()); - StringList RNA_NM_EXTENDED_H2O_modifications(modifications_RNA_NM_EXTENDED_H2O.begin(), modifications_RNA_NM_EXTENDED_H2O.end()); - - StringList RNA_NM_fragments(fragments_RNA_NM.begin(), fragments_RNA_NM.end()); - StringList RNA_NM_fragments_H2O(fragments_RNA_NM_H2O.begin(), fragments_RNA_NM_H2O.end()); - - StringList DNA_DEB_modifications(modifications_DNA_DEB.begin(), modifications_DNA_DEB.end()); - StringList DNA_DEB_EXTENDED_modifications(modifications_DNA_DEB_EXTENDED.begin(), modifications_DNA_DEB_EXTENDED.end()); - StringList DNA_DEB_fragments(fragments_DNA_DEB.begin(), fragments_DNA_DEB.end()); - - StringList DNA_NM_modifications(modifications_DNA_NM.begin(), modifications_DNA_NM.end()); - StringList DNA_NM_EXTENDED_modifications(modifications_DNA_NM_EXTENDED.begin(), modifications_DNA_NM_EXTENDED.end()); - StringList DNA_NM_fragments(fragments_DNA_NM.begin(), fragments_DNA_NM.end()); - - StringList RNA_FA_modifications(modifications_RNA_FA.begin(), modifications_RNA_FA.end()); - StringList RNA_FA_fragments(fragments_RNA_FA.begin(), fragments_RNA_FA.end()); - StringList RNA_FA_EXTENDED_modifications(modifications_RNA_FA_EXTENDED.begin(), modifications_RNA_FA_EXTENDED.end()); - - StringList DNA_FA_modifications(modifications_DNA_FA.begin(), modifications_DNA_FA.end()); - StringList DNA_FA_fragments(fragments_DNA_FA.begin(), fragments_DNA_FA.end()); - StringList DNA_FA_EXTENDED_modifications(modifications_DNA_FA_EXTENDED.begin(), modifications_DNA_FA_EXTENDED.end()); - - StringList DNA_UV_BrU_modifications(modifications_DNA_BrU_UV.begin(), modifications_DNA_BrU_UV.end()); - StringList DNA_UV_BrU_fragments(fragments_DNA_BrU_UV.begin(), fragments_DNA_BrU_UV.end()); - - const String RNA_U = "U"; - const String RNA_UCGA = "UCGA"; - const String DNA_TCGAd = "TCGAd"; - const String RNA_CGA = "CGA"; - const String DNA_CGAd = "CGAd"; - - // set precursor + fragment adducts and cross-linked nucleotide - if (p == "RNA-UV (U)" || p == "RNA-UV (UCGA)") - { - modifications = RNA_UV_modifications; - fragment_adducts = RNA_UV_fragments; - can_cross_link = (p == "RNA-UV (U)") ? RNA_U : RNA_UCGA; - return; - } - else if (p == "RNA-UV Extended (U)" || p == "RNA-UV Extended (UCGA)") - { - modifications = RNA_UV_EXTENDED_modifications; - fragment_adducts = RNA_UV_fragments; - can_cross_link = (p == "RNA-UV Extended (U)") ? RNA_U : RNA_UCGA ; - return; - } - else if (p == "RNA-UV (4SU)") - { - nucleotides.push_back("S=C9H13N2O8PS"); // include 4-Thio-UMP - mapping.push_back("S->S"); - modifications = RNA_UV_4SU_modifications; - fragment_adducts = RNA_UV_4SU_fragments; - can_cross_link = "S"; - return; - } - else if (p == "RNA-UV Extended (4SU)") - { - nucleotides.push_back("S=C9H13N2O8PS"); // include 4-Thio-UMP - mapping.push_back("S->S"); - modifications = RNA_UV_4SU_EXTENDED_modifications; - fragment_adducts = RNA_UV_4SU_fragments; - can_cross_link = "S"; - return; - } - else if (p == "RNA-UV (6SG)") - { - nucleotides.push_back("X=C10H14N5O7PS"); // include 6-Thio-GMP - mapping.push_back("X->X"); - modifications = RNA_UV_6SG_modifications; - fragment_adducts = RNA_UV_6SG_fragments; - can_cross_link = "X"; - return; - } - else if (p == "RNA-UV Extended (6SG)") - { - nucleotides.push_back("X=C10H14N5O7PS"); // include 6-Thio-GMP - mapping.push_back("X->X"); - modifications = RNA_UV_6SG_EXTENDED_modifications; - fragment_adducts = RNA_UV_6SG_fragments; - can_cross_link = "X"; - return; - } - else if (p == "DNA-UV") - { - modifications = DNA_UV_modifications; - fragment_adducts = DNA_UV_fragments; - can_cross_link = DNA_TCGAd; - return; - } - else if (p == "DNA-UV Extended") - { - modifications = DNA_UV_EXTENDED_modifications; - fragment_adducts = DNA_UV_fragments; - can_cross_link = DNA_TCGAd; - return; - } - else if (p == "DNA-UV (BrU)") - { - nucleotides.push_back("B=C9H11N2O8P"); // include BrU - mapping.push_back("B->B"); - modifications = DNA_UV_BrU_modifications; - fragment_adducts = DNA_UV_BrU_fragments; - can_cross_link = "B"; - return; - } - else if (p == "RNA-FA") - { - modifications = RNA_FA_modifications; - fragment_adducts = RNA_FA_fragments; - can_cross_link = RNA_CGA; - return; - } - else if (p == "RNA-FA Extended") - { - modifications = RNA_FA_EXTENDED_modifications; - fragment_adducts = RNA_FA_fragments; - can_cross_link = RNA_CGA; - return; - } - else if (p == "DNA-FA") - { - modifications = DNA_FA_modifications; - fragment_adducts = DNA_FA_fragments; - can_cross_link = DNA_CGAd; - return; - } - else if (p == "DNA-FA Extended") - { - modifications = DNA_FA_EXTENDED_modifications; - fragment_adducts = DNA_FA_fragments; - can_cross_link = DNA_CGAd; - return; - } - else if (p == "RNA-DEB") - { - // add special methionine loss - auto r_ptr = const_cast(ResidueDB::getInstance()->getResidue('M')); - r_ptr->addLossFormula(EmpiricalFormula("CH4S1")); - - modifications = RNA_DEB_modifications; - fragment_adducts = RNA_DEB_fragments; - can_cross_link = RNA_UCGA; - return; - } - else if (p == "RNA-DEB Extended") - { - // add special methionine loss - auto r_ptr = const_cast(ResidueDB::getInstance()->getResidue('M')); - r_ptr->addLossFormula(EmpiricalFormula("CH4S1")); - - modifications = RNA_DEB_EXTENDED_modifications; - fragment_adducts = RNA_DEB_fragments; - can_cross_link = RNA_UCGA; - return; - } - else if (p == "RNA-NM") - { - // add special methionine loss - auto r_ptr = const_cast(ResidueDB::getInstance()->getResidue('M')); - r_ptr->addLossFormula(EmpiricalFormula("CH4S1")); - - modifications = RNA_NM_modifications; - fragment_adducts = RNA_NM_fragments; - can_cross_link = RNA_UCGA; - return; - } - else if (p == "RNA-NM Extended") - { - // add special methionine loss - auto r_ptr = const_cast(ResidueDB::getInstance()->getResidue('M')); - r_ptr->addLossFormula(EmpiricalFormula("CH4S1")); - - modifications = RNA_NM_EXTENDED_modifications; - fragment_adducts = RNA_NM_fragments; - can_cross_link = RNA_UCGA; - return; - } - else if (p == "RNA-NM Extended (+H2O)") - { - // add special methionine loss - auto r_ptr = const_cast(ResidueDB::getInstance()->getResidue('M')); - r_ptr->addLossFormula(EmpiricalFormula("CH4S1")); - - modifications = RNA_NM_EXTENDED_H2O_modifications; - fragment_adducts = RNA_NM_fragments_H2O; - can_cross_link = RNA_UCGA; - return; - } - else if (p == "DNA-DEB") - { - modifications = DNA_DEB_modifications; - fragment_adducts = DNA_DEB_fragments; - can_cross_link = DNA_TCGAd; - return; - } - else if (p == "DNA-DEB Extended") - { - modifications = DNA_DEB_EXTENDED_modifications; - fragment_adducts = DNA_DEB_fragments; - can_cross_link = DNA_TCGAd; - return; - } - else if (p == "DNA-NM") - { - modifications = DNA_NM_modifications; - fragment_adducts = DNA_NM_fragments; - can_cross_link = DNA_TCGAd; - return; - } - else if (p == "DNA-NM Extended") - { - modifications = DNA_NM_EXTENDED_modifications; - fragment_adducts = DNA_NM_fragments; - can_cross_link = DNA_TCGAd; - return; - } - } + String& can_cross_link); + + /** + @brief Get preset parameters for a given preset name (using default presets file) + @param p The preset name + @param nucleotides Output parameter for nucleotides + @param mapping Output parameter for mapping + @param modifications Output parameter for modifications + @param fragment_adducts Output parameter for fragment adducts + @param can_cross_link Output parameter for can_cross_link + */ + OPENMS_DLLAPI void getPresets(const String& p, + StringList& nucleotides, + StringList& mapping, + StringList& modifications, + StringList& fragment_adducts, + String& can_cross_link); } } diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLPresets.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLPresets.cpp new file mode 100644 index 00000000000..aabf865b30c --- /dev/null +++ b/src/openms/source/ANALYSIS/NUXL/NuXLPresets.cpp @@ -0,0 +1,196 @@ +// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin +// SPDX-License-Identifier: BSD-3-Clause +// +// -------------------------------------------------------------------------- +// $Maintainer: Timo Sachsenberg $ +// $Authors: Timo Sachsenberg $ +// -------------------------------------------------------------------------- + +#include +#include +#include +#include + +using json = nlohmann::json; + +namespace OpenMS +{ + namespace NuXLPresets + { + StringList getAllPresetsNames(const String& custom_presets_file) + { + StringList presets; + + // Determine which JSON file to use + String json_path; + if (!custom_presets_file.empty() && File::exists(custom_presets_file)) + { + json_path = custom_presets_file; + OPENMS_LOG_INFO << "Using custom presets file: " << json_path << std::endl; + } + else + { + json_path = File::getOpenMSDataPath() + "/NUXL/nuxl_presets.json"; + } + + if (File::exists(json_path)) + { + OPENMS_LOG_INFO << "Found presets file: " << json_path << std::endl; + } + + if (File::exists(json_path)) + { + try + { + std::ifstream file(json_path.c_str()); + json j; + file >> j; + + // Add all presets to the list + for (auto it = j.begin(); it != j.end(); ++it) + { + presets.push_back(it.key()); + } + } + catch (const std::exception& e) + { + OPENMS_LOG_WARN << "Error reading presets from " << json_path << ": " << e.what() << std::endl; + } + } + else + { + OPENMS_LOG_WARN << "Presets file not found: " << json_path << std::endl; + } + return presets; + } + + void getPresets(const String& p, + const String& custom_presets_file, + StringList& nucleotides, + StringList& mapping, + StringList& modifications, + StringList& fragment_adducts, + String& can_cross_link) + { + StringList presets = getAllPresetsNames(custom_presets_file); + OPENMS_LOG_INFO << "Found presets: " << presets.size() << std::endl; + for (const String& s : presets) + { + OPENMS_LOG_DEBUG << s << std::endl; + } + // Check if preset exists + bool found = find(presets.begin(), presets.end(), p) != presets.end(); + if (!found) + { + throw std::runtime_error("Error: unknown preset '" + p + "'."); + } + + // Try to load presets from JSON file + String json_path; + if (!custom_presets_file.empty() && File::exists(custom_presets_file)) + { + json_path = custom_presets_file; + } + else + { + String share_path = File::getOpenMSDataPath(); + json_path = share_path + "/NUXL/nuxl_presets.json"; + } + + if (File::exists(json_path)) + { + try + { + std::ifstream file(json_path.c_str()); + json j; + file >> j; + + // Check if the requested preset exists in the JSON file + if (j.contains(p.c_str())) + { + const auto& preset = j[p.c_str()]; + + // Load nucleotides + if (preset.contains("target_nucleotides")) + { + nucleotides.clear(); + for (const auto& nuc : preset["target_nucleotides"]) + { + nucleotides.push_back(nuc.get()); + } + } + + // Load mapping + if (preset.contains("mapping")) + { + mapping.clear(); + for (const auto& map : preset["mapping"]) + { + mapping.push_back(map.get()); + } + } + + // Load modifications + if (preset.contains("modifications")) + { + modifications.clear(); + for (const auto& mod : preset["modifications"]) + { + modifications.push_back(mod.get()); + } + } + + // Load fragment adducts + if (preset.contains("fragment_adducts")) + { + fragment_adducts.clear(); + for (const auto& frag : preset["fragment_adducts"]) + { + fragment_adducts.push_back(frag.get()); + } + } + + // Load can_cross_link + if (preset.contains("can_cross_link")) + { + can_cross_link = preset["can_cross_link"].get(); + } + + // Special handling for DEB and NM presets that need methionine loss + if (p.hasSubstring("DEB") || p.hasSubstring("NM")) + { + // add special methionine loss + auto r_ptr = const_cast(ResidueDB::getInstance()->getResidue('M')); + r_ptr->addLossFormula(EmpiricalFormula("CH4S1")); + } + + // Preset loaded successfully, return + OPENMS_LOG_INFO << "Using preset '" << p << "' from " << json_path << std::endl; + return; + } + } + catch (const std::exception& e) + { + // If there's an error reading the JSON file, throw an error + OPENMS_LOG_WARN << "Error reading presets from " << json_path << ": " << e.what() << std::endl; + throw std::runtime_error("Error reading presets."); + } + } + else + { + throw std::runtime_error("Error: presets file not found."); + } + } + + // Overload that uses the default presets file + void getPresets(const String& p, + StringList& nucleotides, + StringList& mapping, + StringList& modifications, + StringList& fragment_adducts, + String& can_cross_link) + { + getPresets(p, "", nucleotides, mapping, modifications, fragment_adducts, can_cross_link); + } + } +} \ No newline at end of file diff --git a/src/openms/source/ANALYSIS/NUXL/sources.cmake b/src/openms/source/ANALYSIS/NUXL/sources.cmake index 460ac2a2607..89240f44388 100644 --- a/src/openms/source/ANALYSIS/NUXL/sources.cmake +++ b/src/openms/source/ANALYSIS/NUXL/sources.cmake @@ -12,6 +12,7 @@ NuXLFragmentIonGenerator.cpp NuXLMarkerIonExtractor.cpp NuXLModificationsGenerator.cpp NuXLParameterParsing.cpp +NuXLPresets.cpp NuXLReport.cpp ) diff --git a/src/topp/OpenNuXL.cpp b/src/topp/OpenNuXL.cpp index 50fd2862b9a..dedbdcd9c67 100644 --- a/src/topp/OpenNuXL.cpp +++ b/src/topp/OpenNuXL.cpp @@ -94,7 +94,6 @@ #include #include - #ifdef _OPENMP #include #define NUMBER_OF_THREADS (omp_get_num_threads()) @@ -888,21 +887,23 @@ class OpenNuXL : // NuXL specific registerTOPPSubsection_("NuXL", "NuXL Options"); - registerStringOption_("NuXL:presets", "